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Repository: CliMA/ClimateMachine.jl
Branch: master
Commit: 2e0b6b7d9771
Files: 670
Total size: 4.3 MB
Directory structure:
gitextract_rqfc0vw8/
├── .buildkite/
│ ├── docs-pipeline.yml
│ └── pipeline.yml
├── .codecov.yml
├── .dev/
│ ├── .gitignore
│ ├── Project.toml
│ ├── clima_formatter_default_image.jl
│ ├── clima_formatter_image.jl
│ ├── clima_formatter_options.jl
│ ├── climaformat.jl
│ ├── hooks/
│ │ ├── pre-commit
│ │ └── pre-commit.sysimage
│ ├── precompile.jl
│ └── systemimage/
│ └── climate_machine_image.jl
├── .github/
│ ├── issue_template.md
│ ├── pull_request_template.md
│ └── workflows/
│ ├── CompatHelper.yml
│ ├── Coverage.yaml
│ ├── DocCleanup.yml
│ ├── Documenter.yaml
│ ├── JuliaFormatter.yml
│ ├── Linux-UnitTests.yml
│ ├── OS-UnitTests.yml
│ ├── PR-Comment.yml
│ └── doc_build_common_error_messages.md
├── .gitignore
├── LICENSE.md
├── Manifest.toml
├── Project.toml
├── README.md
├── bors.toml
├── docs/
│ ├── Manifest.toml
│ ├── Project.toml
│ ├── bibliography.bib
│ ├── clean_build_folder.jl
│ ├── list_of_apis.jl
│ ├── list_of_dev_docs.jl
│ ├── list_of_getting_started_docs.jl
│ ├── list_of_how_to_guides.jl
│ ├── list_of_theory_docs.jl
│ ├── list_of_tutorials.jl
│ ├── make.jl
│ ├── pages_helper.jl
│ ├── plothelpers.jl
│ └── src/
│ ├── APIs/
│ │ ├── Arrays/
│ │ │ └── Arrays.md
│ │ ├── Atmos/
│ │ │ └── AtmosModel.md
│ │ ├── BalanceLaws/
│ │ │ ├── BalanceLaws.md
│ │ │ └── Problems.md
│ │ ├── Common/
│ │ │ ├── CartesianDomains.md
│ │ │ ├── CartesianFields.md
│ │ │ ├── Orientations.md
│ │ │ ├── Spectra.md
│ │ │ ├── TurbulenceClosures.md
│ │ │ └── TurbulenceConvection.md
│ │ ├── Diagnostics/
│ │ │ ├── Diagnostics.md
│ │ │ ├── DiagnosticsMachine.md
│ │ │ ├── StateCheck.md
│ │ │ └── StdDiagnostics.md
│ │ ├── Driver/
│ │ │ ├── Checkpoint.md
│ │ │ └── index.md
│ │ ├── InputOutput/
│ │ │ └── index.md
│ │ ├── Land/
│ │ │ ├── LandModel.md
│ │ │ ├── RadiativeEnergyFlux.md
│ │ │ ├── Runoff.md
│ │ │ ├── SoilHeatParameterizations.md
│ │ │ ├── SoilWaterParameterizations.md
│ │ │ └── SurfaceFlow.md
│ │ ├── Numerics/
│ │ │ ├── DGMethods/
│ │ │ │ ├── Courant.md
│ │ │ │ ├── DGMethods.md
│ │ │ │ ├── FVReconstructions.md
│ │ │ │ └── NumericalFluxes.md
│ │ │ ├── Meshes/
│ │ │ │ └── Mesh.md
│ │ │ ├── ODESolvers/
│ │ │ │ └── ODESolvers.md
│ │ │ └── SystemSolvers/
│ │ │ └── SystemSolvers.md
│ │ ├── Ocean/
│ │ │ └── Ocean.md
│ │ ├── Utilities/
│ │ │ ├── SingleStackUtils.md
│ │ │ ├── TicToc.md
│ │ │ └── VariableTemplates.md
│ │ └── index.md
│ ├── Contributing.md
│ ├── DevDocs/
│ │ ├── AcceptableUnicode.md
│ │ ├── CodeStyle.md
│ │ ├── DiagnosticVariableList.md
│ │ ├── ModelOutput.md
│ │ ├── ModelVariableList.md
│ │ └── SystemImage.md
│ ├── GettingStarted/
│ │ ├── Atmos.md
│ │ ├── Installation.md
│ │ ├── RunningClimateMachine.md
│ │ └── Terminology.md
│ ├── HowToGuides/
│ │ ├── Atmos/
│ │ │ ├── AtmosReferenceState.md
│ │ │ ├── MoistureAndPrecip.md
│ │ │ ├── MoistureModelChoices.md
│ │ │ └── PrecipitationModelChoices.md
│ │ ├── BalanceLaws/
│ │ │ └── how_to_make_a_balance_law.md
│ │ ├── Diagnostics/
│ │ │ └── UsingDiagnostics.md
│ │ ├── Land/
│ │ │ └── index.md
│ │ ├── Numerics/
│ │ │ ├── Meshes/
│ │ │ │ └── index.md
│ │ │ ├── ODESolvers/
│ │ │ │ └── Timestepping.md
│ │ │ └── SystemSolvers/
│ │ │ └── IterativeSolvers.md
│ │ └── Ocean/
│ │ └── index.md
│ ├── References.md
│ ├── Theory/
│ │ ├── Atmos/
│ │ │ ├── AtmosModel.md
│ │ │ ├── EDMFEquations.md
│ │ │ ├── EDMF_plots.md
│ │ │ ├── Microphysics_0M.md
│ │ │ ├── Microphysics_1M.md
│ │ │ └── Model/
│ │ │ └── tracers.md
│ │ └── Common/
│ │ └── Turbulence.md
│ └── index.md
├── experiments/
│ ├── AtmosGCM/
│ │ ├── GCMDriver/
│ │ │ ├── GCMDriver.jl
│ │ │ ├── baroclinicwave_problem.jl
│ │ │ ├── gcm_base_states.jl
│ │ │ ├── gcm_bcs.jl
│ │ │ ├── gcm_moisture_profiles.jl
│ │ │ ├── gcm_perturbations.jl
│ │ │ ├── gcm_sources.jl
│ │ │ └── heldsuarez_problem.jl
│ │ ├── heldsuarez.jl
│ │ ├── moist_baroclinic_wave_bulksfcflux.jl
│ │ └── nonhydrostatic_gravity_wave.jl
│ ├── AtmosLES/
│ │ ├── Artifacts.toml
│ │ ├── bomex_les.jl
│ │ ├── bomex_model.jl
│ │ ├── bomex_single_stack.jl
│ │ ├── cfsite_hadgem2-a_07_amip.jl
│ │ ├── convective_bl_les.jl
│ │ ├── convective_bl_model.jl
│ │ ├── dycoms.jl
│ │ ├── ekman_layer_model.jl
│ │ ├── rising_bubble_bryan.jl
│ │ ├── rising_bubble_theta_formulation.jl
│ │ ├── schar_scalar_advection.jl
│ │ ├── squall_line.jl
│ │ ├── stable_bl_les.jl
│ │ ├── stable_bl_model.jl
│ │ ├── surfacebubble.jl
│ │ └── taylor_green.jl
│ ├── OceanBoxGCM/
│ │ ├── homogeneous_box.jl
│ │ ├── ocean_gyre.jl
│ │ └── simple_box.jl
│ ├── OceanSplitExplicit/
│ │ └── simple_box.jl
│ └── TestCase/
│ ├── baroclinic_wave.jl
│ ├── baroclinic_wave_fvm.jl
│ ├── isothermal_zonal_flow.jl
│ ├── risingbubble.jl
│ ├── risingbubble_fvm.jl
│ ├── solid_body_rotation.jl
│ ├── solid_body_rotation_fvm.jl
│ └── solid_body_rotation_mountain.jl
├── src/
│ ├── Arrays/
│ │ ├── CMBuffers.jl
│ │ └── MPIStateArrays.jl
│ ├── Atmos/
│ │ ├── Model/
│ │ │ ├── AtmosModel.jl
│ │ │ ├── atmos_tendencies.jl
│ │ │ ├── bc_energy.jl
│ │ │ ├── bc_initstate.jl
│ │ │ ├── bc_moisture.jl
│ │ │ ├── bc_momentum.jl
│ │ │ ├── bc_precipitation.jl
│ │ │ ├── bc_tracer.jl
│ │ │ ├── boundaryconditions.jl
│ │ │ ├── courant.jl
│ │ │ ├── declare_prognostic_vars.jl
│ │ │ ├── energy.jl
│ │ │ ├── filters.jl
│ │ │ ├── get_prognostic_vars.jl
│ │ │ ├── linear.jl
│ │ │ ├── linear_atmos_tendencies.jl
│ │ │ ├── linear_tendencies.jl
│ │ │ ├── lsforcing.jl
│ │ │ ├── moisture.jl
│ │ │ ├── multiphysics_types.jl
│ │ │ ├── precipitation.jl
│ │ │ ├── problem.jl
│ │ │ ├── prog_prim_conversion.jl
│ │ │ ├── projections.jl
│ │ │ ├── radiation.jl
│ │ │ ├── reconstructions.jl
│ │ │ ├── ref_state.jl
│ │ │ ├── tendencies_energy.jl
│ │ │ ├── tendencies_mass.jl
│ │ │ ├── tendencies_moisture.jl
│ │ │ ├── tendencies_momentum.jl
│ │ │ ├── tendencies_precipitation.jl
│ │ │ ├── tendencies_tracers.jl
│ │ │ ├── thermo_states.jl
│ │ │ ├── thermo_states_anelastic.jl
│ │ │ └── tracers.jl
│ │ ├── Parameterizations/
│ │ │ ├── GravityWaves/
│ │ │ │ └── README.md
│ │ │ ├── README.md
│ │ │ └── Radiation/
│ │ │ └── README.md
│ │ └── TemperatureProfiles/
│ │ └── TemperatureProfiles.jl
│ ├── BalanceLaws/
│ │ ├── BalanceLaws.jl
│ │ ├── Problems.jl
│ │ ├── boundaryconditions.jl
│ │ ├── interface.jl
│ │ ├── kernels.jl
│ │ ├── prog_prim_conversion.jl
│ │ ├── show_tendencies.jl
│ │ ├── state_types.jl
│ │ ├── sum_tendencies.jl
│ │ ├── tendency_types.jl
│ │ └── vars_wrappers.jl
│ ├── ClimateMachine.jl
│ ├── Common/
│ │ ├── CartesianDomains/
│ │ │ ├── CartesianDomains.jl
│ │ │ └── rectangular_domain.jl
│ │ ├── CartesianFields/
│ │ │ ├── CartesianFields.jl
│ │ │ ├── rectangular_element.jl
│ │ │ └── rectangular_spectral_element_fields.jl
│ │ ├── Orientations/
│ │ │ └── Orientations.jl
│ │ ├── Spectra/
│ │ │ ├── Spectra.jl
│ │ │ ├── power_spectrum_gcm.jl
│ │ │ ├── power_spectrum_les.jl
│ │ │ └── spherical_helper.jl
│ │ ├── SurfaceFluxes/
│ │ │ └── README.md
│ │ ├── TurbulenceClosures/
│ │ │ └── TurbulenceClosures.jl
│ │ └── TurbulenceConvection/
│ │ ├── TurbulenceConvection.jl
│ │ ├── boundary_conditions.jl
│ │ └── source.jl
│ ├── Diagnostics/
│ │ ├── Debug/
│ │ │ └── StateCheck.jl
│ │ ├── Diagnostics.jl
│ │ ├── DiagnosticsMachine/
│ │ │ ├── DiagnosticsMachine.jl
│ │ │ ├── atmos_diagnostic_funs.jl
│ │ │ ├── group_gen.jl
│ │ │ ├── groups.jl
│ │ │ ├── horizontal_average.jl
│ │ │ ├── onetime.jl
│ │ │ ├── pointwise.jl
│ │ │ └── variables.jl
│ │ ├── StdDiagnostics/
│ │ │ ├── StdDiagnostics.jl
│ │ │ ├── atmos_gcm_default.jl
│ │ │ ├── atmos_gcm_diagnostic_vars.jl
│ │ │ ├── atmos_les_default.jl
│ │ │ └── atmos_les_diagnostic_vars.jl
│ │ ├── atmos_common.jl
│ │ ├── atmos_gcm_default.jl
│ │ ├── atmos_gcm_spectra.jl
│ │ ├── atmos_les_core.jl
│ │ ├── atmos_les_default.jl
│ │ ├── atmos_les_default_perturbations.jl
│ │ ├── atmos_les_spectra.jl
│ │ ├── atmos_mass_energy_loss.jl
│ │ ├── atmos_refstate_perturbations.jl
│ │ ├── atmos_turbulence_stats.jl
│ │ ├── diagnostic_fields.jl
│ │ ├── dump_aux.jl
│ │ ├── dump_init.jl
│ │ ├── dump_state.jl
│ │ ├── dump_tendencies.jl
│ │ ├── groups.jl
│ │ ├── helpers.jl
│ │ ├── thermo.jl
│ │ ├── variables.jl
│ │ └── vorticity_balancelaw.jl
│ ├── Driver/
│ │ ├── Callbacks/
│ │ │ └── Callbacks.jl
│ │ ├── Checkpoint/
│ │ │ └── Checkpoint.jl
│ │ ├── ConfigTypes/
│ │ │ └── ConfigTypes.jl
│ │ ├── Driver.jl
│ │ ├── SolverTypes/
│ │ │ ├── ExplicitSolverType.jl
│ │ │ ├── HEVISolverType.jl
│ │ │ ├── IMEXSolverType.jl
│ │ │ ├── ImplicitSolverType.jl
│ │ │ ├── MISSolverType.jl
│ │ │ ├── MultirateSolverType.jl
│ │ │ ├── SolverTypes.jl
│ │ │ └── SplitExplicitSolverType.jl
│ │ ├── diagnostics_configs.jl
│ │ ├── driver_configs.jl
│ │ ├── solver_config_wrappers.jl
│ │ └── solver_configs.jl
│ ├── InputOutput/
│ │ ├── VTK/
│ │ │ ├── VTK.jl
│ │ │ ├── fieldwriter.jl
│ │ │ ├── writemesh.jl
│ │ │ ├── writepvtu.jl
│ │ │ └── writevtk.jl
│ │ └── Writers/
│ │ ├── Writers.jl
│ │ └── netcdf_writer.jl
│ ├── LICENSE
│ ├── Land/
│ │ └── Model/
│ │ ├── LandModel.jl
│ │ ├── RadiativeEnergyFlux.jl
│ │ ├── Runoff.jl
│ │ ├── SoilHeatParameterizations.jl
│ │ ├── SoilWaterParameterizations.jl
│ │ ├── SurfaceFlow.jl
│ │ ├── land_bc.jl
│ │ ├── land_tendencies.jl
│ │ ├── prog_types.jl
│ │ ├── prognostic_vars.jl
│ │ ├── soil_bc.jl
│ │ ├── soil_heat.jl
│ │ ├── soil_model.jl
│ │ ├── soil_water.jl
│ │ └── source.jl
│ ├── Numerics/
│ │ ├── DGMethods/
│ │ │ ├── Courant.jl
│ │ │ ├── DGFVModel.jl
│ │ │ ├── DGFVModel_kernels.jl
│ │ │ ├── DGMethods.jl
│ │ │ ├── DGModel.jl
│ │ │ ├── DGModel_kernels.jl
│ │ │ ├── ESDGModel.jl
│ │ │ ├── ESDGModel_kernels.jl
│ │ │ ├── FVReconstructions.jl
│ │ │ ├── NumericalFluxes.jl
│ │ │ ├── SpaceDiscretization.jl
│ │ │ ├── create_states.jl
│ │ │ ├── custom_filter.jl
│ │ │ └── remainder.jl
│ │ ├── Mesh/
│ │ │ ├── BrickMesh.jl
│ │ │ ├── DSS.jl
│ │ │ ├── Elements.jl
│ │ │ ├── Filters.jl
│ │ │ ├── GeometricFactors.jl
│ │ │ ├── Geometry.jl
│ │ │ ├── Grids.jl
│ │ │ ├── Interpolation.jl
│ │ │ ├── Mesh.jl
│ │ │ ├── Metrics.jl
│ │ │ └── Topologies.jl
│ │ ├── ODESolvers/
│ │ │ ├── AdditiveRungeKuttaMethod.jl
│ │ │ ├── BackwardEulerSolvers.jl
│ │ │ ├── DifferentialEquations.jl
│ │ │ ├── GenericCallbacks.jl
│ │ │ ├── LowStorageRungeKutta3NMethod.jl
│ │ │ ├── LowStorageRungeKuttaMethod.jl
│ │ │ ├── MultirateInfinitesimalGARKDecoupledImplicit.jl
│ │ │ ├── MultirateInfinitesimalGARKExplicit.jl
│ │ │ ├── MultirateInfinitesimalStepMethod.jl
│ │ │ ├── MultirateRungeKuttaMethod.jl
│ │ │ ├── ODESolvers.jl
│ │ │ ├── SplitExplicitMethod.jl
│ │ │ └── StrongStabilityPreservingRungeKuttaMethod.jl
│ │ └── SystemSolvers/
│ │ ├── SystemSolvers.jl
│ │ ├── batched_generalized_minimal_residual_solver.jl
│ │ ├── columnwise_lu_solver.jl
│ │ ├── conjugate_gradient_solver.jl
│ │ ├── generalized_conjugate_residual_solver.jl
│ │ ├── generalized_minimal_residual_solver.jl
│ │ ├── jacobian_free_newton_krylov_solver.jl
│ │ └── preconditioners.jl
│ ├── Ocean/
│ │ ├── HydrostaticBoussinesq/
│ │ │ ├── Courant.jl
│ │ │ ├── HydrostaticBoussinesq.jl
│ │ │ ├── LinearHBModel.jl
│ │ │ ├── bc_temperature.jl
│ │ │ ├── bc_velocity.jl
│ │ │ └── hydrostatic_boussinesq_model.jl
│ │ ├── JLD2Writer.jl
│ │ ├── Ocean.jl
│ │ ├── OceanBC.jl
│ │ ├── OceanProblems/
│ │ │ ├── OceanProblems.jl
│ │ │ ├── homogeneous_box.jl
│ │ │ ├── initial_value_problem.jl
│ │ │ ├── ocean_gyre.jl
│ │ │ ├── shallow_water_initial_states.jl
│ │ │ └── simple_box_problem.jl
│ │ ├── README.md
│ │ ├── ShallowWater/
│ │ │ ├── ShallowWaterModel.jl
│ │ │ └── bc_velocity.jl
│ │ ├── SplitExplicit/
│ │ │ ├── Communication.jl
│ │ │ ├── HydrostaticBoussinesqCoupling.jl
│ │ │ ├── ShallowWaterCoupling.jl
│ │ │ ├── SplitExplicitModel.jl
│ │ │ └── VerticalIntegralModel.jl
│ │ ├── SplitExplicit01/
│ │ │ ├── BarotropicModel.jl
│ │ │ ├── Communication.jl
│ │ │ ├── Continuity3dModel.jl
│ │ │ ├── IVDCModel.jl
│ │ │ ├── OceanBoundaryConditions.jl
│ │ │ ├── OceanModel.jl
│ │ │ ├── SplitExplicitLSRK2nMethod.jl
│ │ │ ├── SplitExplicitLSRK3nMethod.jl
│ │ │ ├── SplitExplicitModel.jl
│ │ │ └── VerticalIntegralModel.jl
│ │ └── SuperModels.jl
│ └── Utilities/
│ ├── SingleStackUtils/
│ │ ├── SingleStackUtils.jl
│ │ └── single_stack_diagnostics.jl
│ ├── TicToc/
│ │ └── TicToc.jl
│ └── VariableTemplates/
│ ├── VariableTemplates.jl
│ ├── flattened_tup_chain.jl
│ └── var_names.jl
├── test/
│ ├── Arrays/
│ │ ├── basics.jl
│ │ ├── broadcasting.jl
│ │ ├── mpi_comm.jl
│ │ ├── reductions.jl
│ │ ├── runtests.jl
│ │ └── varsindex.jl
│ ├── Atmos/
│ │ ├── EDMF/
│ │ │ ├── Artifacts.toml
│ │ │ ├── bomex_edmf.jl
│ │ │ ├── closures/
│ │ │ │ ├── entr_detr.jl
│ │ │ │ ├── mixing_length.jl
│ │ │ │ ├── pressure.jl
│ │ │ │ ├── surface_functions.jl
│ │ │ │ └── turbulence_functions.jl
│ │ │ ├── compute_mse.jl
│ │ │ ├── edmf_kernels.jl
│ │ │ ├── edmf_model.jl
│ │ │ ├── ekman_layer.jl
│ │ │ ├── helper_funcs/
│ │ │ │ ├── diagnose_environment.jl
│ │ │ │ ├── diagnostics_configuration.jl
│ │ │ │ ├── lamb_smooth_minimum.jl
│ │ │ │ ├── nondimensional_exchange_functions.jl
│ │ │ │ ├── save_subdomain_temperature.jl
│ │ │ │ ├── subdomain_statistics.jl
│ │ │ │ ├── subdomain_thermo_states.jl
│ │ │ │ └── utility_funcs.jl
│ │ │ ├── report_mse_bomex.jl
│ │ │ ├── report_mse_sbl_anelastic.jl
│ │ │ ├── report_mse_sbl_coupled_edmf_an1d.jl
│ │ │ ├── report_mse_sbl_edmf.jl
│ │ │ ├── report_mse_sbl_ss_implicit.jl
│ │ │ ├── stable_bl_anelastic1d.jl
│ │ │ ├── stable_bl_coupled_edmf_an1d.jl
│ │ │ ├── stable_bl_edmf.jl
│ │ │ ├── stable_bl_edmf_fvm.jl
│ │ │ ├── stable_bl_single_stack_implicit.jl
│ │ │ └── variable_map.jl
│ │ ├── Model/
│ │ │ ├── Artifacts.toml
│ │ │ ├── discrete_hydrostatic_balance.jl
│ │ │ ├── get_atmos_ref_states.jl
│ │ │ ├── ref_state.jl
│ │ │ └── runtests.jl
│ │ ├── Parameterizations/
│ │ │ └── Microphysics/
│ │ │ ├── KM_ice.jl
│ │ │ ├── KM_saturation_adjustment.jl
│ │ │ ├── KM_warm_rain.jl
│ │ │ └── KinematicModel.jl
│ │ ├── prog_prim_conversion/
│ │ │ └── runtests.jl
│ │ └── runtests.jl
│ ├── BalanceLaws/
│ │ └── runtests.jl
│ ├── Common/
│ │ ├── CartesianDomains/
│ │ │ └── runtests.jl
│ │ ├── CartesianFields/
│ │ │ └── runtests.jl
│ │ ├── Spectra/
│ │ │ ├── gcm_standalone_visual_test.jl
│ │ │ ├── runtests.jl
│ │ │ └── spherical_helper_test.jl
│ │ └── runtests.jl
│ ├── Diagnostics/
│ │ ├── Debug/
│ │ │ ├── test_statecheck.jl
│ │ │ └── test_statecheck_refvals.jl
│ │ ├── diagnostic_fields_test.jl
│ │ ├── dm_tests.jl
│ │ ├── runtests.jl
│ │ ├── sin_init.jl
│ │ └── sin_test.jl
│ ├── Driver/
│ │ ├── cr_unit_tests.jl
│ │ ├── gcm_driver_test.jl
│ │ ├── les_driver_test.jl
│ │ ├── mms3.jl
│ │ └── runtests.jl
│ ├── InputOutput/
│ │ ├── VTK/
│ │ │ └── runtests.jl
│ │ ├── Writers/
│ │ │ └── runtests.jl
│ │ └── runtests.jl
│ ├── Land/
│ │ ├── Model/
│ │ │ ├── Artifacts.toml
│ │ │ ├── freeze_thaw_alone.jl
│ │ │ ├── haverkamp_test.jl
│ │ │ ├── heat_analytic_unit_test.jl
│ │ │ ├── prescribed_twice.jl
│ │ │ ├── runtests.jl
│ │ │ ├── soil_heterogeneity.jl
│ │ │ ├── test_bc.jl
│ │ │ ├── test_bc_3d.jl
│ │ │ ├── test_heat_parameterizations.jl
│ │ │ ├── test_overland_flow_analytic.jl
│ │ │ ├── test_overland_flow_vcatchment.jl
│ │ │ ├── test_physical_bc.jl
│ │ │ ├── test_radiative_energy_flux_functions.jl
│ │ │ └── test_water_parameterizations.jl
│ │ └── runtests.jl
│ ├── Numerics/
│ │ ├── DGMethods/
│ │ │ ├── Euler/
│ │ │ │ ├── acousticwave_1d_imex.jl
│ │ │ │ ├── acousticwave_mrigark.jl
│ │ │ │ ├── acousticwave_variable_degree.jl
│ │ │ │ ├── fvm_balance.jl
│ │ │ │ ├── fvm_isentropicvortex.jl
│ │ │ │ ├── isentropicvortex.jl
│ │ │ │ ├── isentropicvortex_imex.jl
│ │ │ │ ├── isentropicvortex_lmars.jl
│ │ │ │ ├── isentropicvortex_mrigark.jl
│ │ │ │ ├── isentropicvortex_mrigark_implicit.jl
│ │ │ │ ├── isentropicvortex_multirate.jl
│ │ │ │ └── isentropicvortex_setup.jl
│ │ │ ├── advection_diffusion/
│ │ │ │ ├── advection_diffusion_model.jl
│ │ │ │ ├── advection_diffusion_model_1dimex_bgmres.jl
│ │ │ │ ├── advection_diffusion_model_1dimex_bjfnks.jl
│ │ │ │ ├── advection_sphere.jl
│ │ │ │ ├── diffusion_hyperdiffusion_sphere.jl
│ │ │ │ ├── direction_splitting_advection_diffusion.jl
│ │ │ │ ├── fvm_advection.jl
│ │ │ │ ├── fvm_advection_diffusion.jl
│ │ │ │ ├── fvm_advection_diffusion_model_1dimex_bjfnks.jl
│ │ │ │ ├── fvm_advection_diffusion_periodic.jl
│ │ │ │ ├── fvm_advection_sphere.jl
│ │ │ │ ├── fvm_swirl.jl
│ │ │ │ ├── hyperdiffusion_bc.jl
│ │ │ │ ├── hyperdiffusion_model.jl
│ │ │ │ ├── periodic_3D_hyperdiffusion.jl
│ │ │ │ ├── pseudo1D_advection_diffusion.jl
│ │ │ │ ├── pseudo1D_advection_diffusion_1dimex.jl
│ │ │ │ ├── pseudo1D_advection_diffusion_mrigark_implicit.jl
│ │ │ │ ├── pseudo1D_heat_eqn.jl
│ │ │ │ └── variable_degree_advection_diffusion.jl
│ │ │ ├── compressible_Navier_Stokes/
│ │ │ │ ├── density_current_model.jl
│ │ │ │ ├── mms_bc_atmos.jl
│ │ │ │ ├── mms_bc_dgmodel.jl
│ │ │ │ ├── mms_model.jl
│ │ │ │ ├── mms_solution.jl
│ │ │ │ └── mms_solution_generated.jl
│ │ │ ├── compressible_navier_stokes_equations/
│ │ │ │ ├── plotting/
│ │ │ │ │ ├── bigfileofstuff.jl
│ │ │ │ │ ├── plot_output.jl
│ │ │ │ │ └── vizinanigans.jl
│ │ │ │ ├── shared_source/
│ │ │ │ │ ├── FluidBC.jl
│ │ │ │ │ ├── ScalarFields.jl
│ │ │ │ │ ├── VectorFields.jl
│ │ │ │ │ ├── abstractions.jl
│ │ │ │ │ ├── boilerplate.jl
│ │ │ │ │ ├── callbacks.jl
│ │ │ │ │ ├── domains.jl
│ │ │ │ │ └── grids.jl
│ │ │ │ ├── sphere/
│ │ │ │ │ ├── sphere_helper_functions.jl
│ │ │ │ │ ├── test_heat_equation.jl
│ │ │ │ │ ├── test_hydrostatic_balance.jl
│ │ │ │ │ └── test_sphere.jl
│ │ │ │ ├── three_dimensional/
│ │ │ │ │ ├── ThreeDimensionalCompressibleNavierStokesEquations.jl
│ │ │ │ │ ├── bc_momentum.jl
│ │ │ │ │ ├── bc_temperature.jl
│ │ │ │ │ ├── config_sphere.jl
│ │ │ │ │ ├── refvals_bickley_jet.jl
│ │ │ │ │ ├── refvals_buoyancy.jl
│ │ │ │ │ ├── run_bickley_jet.jl
│ │ │ │ │ ├── run_box.jl
│ │ │ │ │ ├── run_taylor_green_vortex.jl
│ │ │ │ │ ├── test_bickley_jet.jl
│ │ │ │ │ └── test_buoyancy.jl
│ │ │ │ └── two_dimensional/
│ │ │ │ ├── TwoDimensionalCompressibleNavierStokesEquations.jl
│ │ │ │ ├── bc_momentum.jl
│ │ │ │ ├── bc_tracer.jl
│ │ │ │ ├── refvals_bickley_jet.jl
│ │ │ │ ├── run_bickley_jet.jl
│ │ │ │ └── test_bickley_jet.jl
│ │ │ ├── conservation/
│ │ │ │ └── sphere.jl
│ │ │ ├── courant.jl
│ │ │ ├── custom_filter.jl
│ │ │ ├── fv_reconstruction_test.jl
│ │ │ ├── grad_test.jl
│ │ │ ├── grad_test_sphere.jl
│ │ │ ├── horizontal_integral_test.jl
│ │ │ ├── integral_test.jl
│ │ │ ├── integral_test_sphere.jl
│ │ │ ├── remainder_model.jl
│ │ │ └── vars_test.jl
│ │ ├── ESDGMethods/
│ │ │ ├── DryAtmos/
│ │ │ │ ├── DryAtmos.jl
│ │ │ │ ├── baroclinic_wave.jl
│ │ │ │ ├── linear.jl
│ │ │ │ ├── run_tests.jl
│ │ │ │ └── run_tests_mpo.jl
│ │ │ └── diagnostics.jl
│ │ ├── Mesh/
│ │ │ ├── BrickMesh.jl
│ │ │ ├── DSS.jl
│ │ │ ├── DSS_mpi.jl
│ │ │ ├── Elements.jl
│ │ │ ├── Geometry.jl
│ │ │ ├── Grids.jl
│ │ │ ├── Metrics.jl
│ │ │ ├── filter.jl
│ │ │ ├── filter_TMAR.jl
│ │ │ ├── grid_integral.jl
│ │ │ ├── interpolation.jl
│ │ │ ├── min_node_distance.jl
│ │ │ ├── mpi_centroid.jl
│ │ │ ├── mpi_connect.jl
│ │ │ ├── mpi_connect_1d.jl
│ │ │ ├── mpi_connect_ell.jl
│ │ │ ├── mpi_connect_sphere.jl
│ │ │ ├── mpi_connect_stacked.jl
│ │ │ ├── mpi_connect_stacked_3d.jl
│ │ │ ├── mpi_connectfull.jl
│ │ │ ├── mpi_getpartition.jl
│ │ │ ├── mpi_partition.jl
│ │ │ ├── mpi_sortcolumns.jl
│ │ │ └── topology.jl
│ │ ├── ODESolvers/
│ │ │ ├── callbacks.jl
│ │ │ ├── ode_tests_basic.jl
│ │ │ ├── ode_tests_common.jl
│ │ │ ├── ode_tests_convergence.jl
│ │ │ └── runtests.jl
│ │ ├── SystemSolvers/
│ │ │ ├── bandedsystem.jl
│ │ │ ├── bgmres.jl
│ │ │ ├── cg.jl
│ │ │ ├── columnwiselu.jl
│ │ │ ├── iterativesolvers.jl
│ │ │ ├── poisson.jl
│ │ │ └── runtests.jl
│ │ └── runtests.jl
│ ├── Ocean/
│ │ ├── HydrostaticBoussinesq/
│ │ │ ├── test_3D_spindown.jl
│ │ │ ├── test_initial_value_problem.jl
│ │ │ ├── test_ocean_gyre_long.jl
│ │ │ ├── test_ocean_gyre_short.jl
│ │ │ ├── test_windstress_long.jl
│ │ │ └── test_windstress_short.jl
│ │ ├── HydrostaticBoussinesqModel/
│ │ │ └── test_hydrostatic_boussinesq_model.jl
│ │ ├── OceanProblems/
│ │ │ └── test_initial_value_problem.jl
│ │ ├── ShallowWater/
│ │ │ ├── GyreDriver.jl
│ │ │ └── test_2D_spindown.jl
│ │ ├── SplitExplicit/
│ │ │ ├── hydrostatic_spindown.jl
│ │ │ ├── simple_box_2dt.jl
│ │ │ ├── simple_box_ivd.jl
│ │ │ ├── simple_box_rk3.jl
│ │ │ ├── simple_dbl_gyre.jl
│ │ │ ├── split_explicit.jl
│ │ │ ├── test_coriolis.jl
│ │ │ ├── test_restart.jl
│ │ │ ├── test_simple_box.jl
│ │ │ ├── test_spindown_long.jl
│ │ │ ├── test_spindown_short.jl
│ │ │ └── test_vertical_integral_model.jl
│ │ ├── refvals/
│ │ │ ├── 2D_hydrostatic_spindown_refvals.jl
│ │ │ ├── 3D_hydrostatic_spindown_refvals.jl
│ │ │ ├── hydrostatic_spindown_refvals.jl
│ │ │ ├── simple_box_2dt_refvals.jl
│ │ │ ├── simple_box_ivd_refvals.jl
│ │ │ ├── simple_box_rk3_refvals.jl
│ │ │ ├── simple_dbl_gyre_refvals.jl
│ │ │ ├── test_ocean_gyre_refvals.jl
│ │ │ ├── test_vertical_integral_model_refvals.jl
│ │ │ └── test_windstress_refvals.jl
│ │ └── runtests.jl
│ ├── Utilities/
│ │ ├── SingleStackUtils/
│ │ │ ├── runtests.jl
│ │ │ └── ssu_tests.jl
│ │ ├── TicToc/
│ │ │ └── runtests.jl
│ │ ├── VariableTemplates/
│ │ │ ├── complex_models.jl
│ │ │ ├── runtests.jl
│ │ │ ├── runtests_gpu.jl
│ │ │ ├── test_base_functionality.jl
│ │ │ ├── test_complex_models.jl
│ │ │ ├── test_complex_models_gpu.jl
│ │ │ └── varsindex.jl
│ │ └── runtests.jl
│ ├── runtests.jl
│ ├── runtests_gpu.jl
│ └── testhelpers.jl
└── tutorials/
├── Atmos/
│ ├── agnesi_hs_lin.jl
│ ├── agnesi_nh_lin.jl
│ ├── burgers_single_stack.jl
│ ├── burgers_single_stack_bjfnk.jl
│ ├── burgers_single_stack_fvm.jl
│ ├── densitycurrent.jl
│ ├── dry_rayleigh_benard.jl
│ ├── heldsuarez.jl
│ └── risingbubble.jl
├── BalanceLaws/
│ └── tendency_specification_layer.jl
├── Diagnostics/
│ └── Debug/
│ └── StateCheck.jl
├── Land/
│ ├── Heat/
│ │ └── heat_equation.jl
│ └── Soil/
│ ├── Artifacts.toml
│ ├── Coupled/
│ │ └── equilibrium_test.jl
│ ├── Heat/
│ │ └── bonan_heat_tutorial.jl
│ ├── PhaseChange/
│ │ ├── freezing_front.jl
│ │ └── phase_change_analytic_test.jl
│ ├── Water/
│ │ ├── equilibrium_test.jl
│ │ └── hydraulic_functions.jl
│ └── interpolation_helper.jl
├── Numerics/
│ ├── DGMethods/
│ │ ├── Box1D.jl
│ │ └── showcase_filters.jl
│ ├── SystemSolvers/
│ │ ├── bgmres.jl
│ │ └── cg.jl
│ └── TimeStepping/
│ ├── explicit_lsrk.jl
│ ├── imex_ark.jl
│ ├── mis.jl
│ ├── multirate_rk.jl
│ ├── ts_intro.jl
│ ├── tutorial_acousticwave_config.jl
│ └── tutorial_risingbubble_config.jl
├── Ocean/
│ ├── geostrophic_adjustment.jl
│ ├── internal_wave.jl
│ └── shear_instability.jl
├── TutorialList.jl
└── literate_markdown.jl
================================================
FILE CONTENTS
================================================
================================================
FILE: .buildkite/docs-pipeline.yml
================================================
env:
JULIA_VERSION: "1.5.4"
GKSwstype: nul
OPENBLAS_NUM_THREADS: 1
CLIMATEMACHINE_SETTINGS_DISABLE_GPU: "true"
CLIMATEMACHINE_SETTINGS_FIX_RNG_SEED: "true"
CLIMATEMACHINE_SETTINGS_DISABLE_CUSTOM_LOGGER: "true"
steps:
- label: "Build project"
command:
- "julia --project --color=yes -e 'using Pkg; Pkg.instantiate()'"
- "julia --project=docs/ --color=yes -e 'using Pkg; Pkg.instantiate()'"
- "julia --project=docs/ --color=yes -e 'using Pkg; Pkg.precompile()'"
agents:
config: cpu
queue: central
slurm_ntasks: 1
slurm_cpus_per_task: 1
slurm_mem_per_cpu: 6000
- wait
- label: "Build docs"
command:
# this extracts out the PR number from the bors message on the trying branch
# to force documenter to deploy the PR branch number gh-preview
- "if [ $$BUILDKITE_BRANCH == \"trying\" ]; then \
export BUILDKITE_PULL_REQUEST=\"$${BUILDKITE_MESSAGE//[!0-9]/}\"; \
fi"
- "if [[ ! -z \"$${PULL_REQUEST}\" ]]; then \
export BUILDKITE_PULL_REQUEST=\"$${PULL_REQUEST}\"; \
fi"
- "julia --project=docs/ --color=yes --procs=10 docs/make.jl"
env:
JULIA_PROJECT: "docs/"
agents:
config: cpu
queue: central
slurm_time: 120
slurm_nodes: 1
slurm_ntasks: 10
slurm_cpus_per_task: 1
slurm_mem_per_cpu: 6000
================================================
FILE: .buildkite/pipeline.yml
================================================
env:
JULIA_VERSION: "1.5.4"
OPENMPI_VERSION: "4.0.4"
CUDA_VERSION: "10.2"
OPENBLAS_NUM_THREADS: 1
CLIMATEMACHINE_SETTINGS_FIX_RNG_SEED: "true"
steps:
- label: "init cpu env"
key: "init_cpu_env"
command:
- "echo $JULIA_DEPOT_PATH"
- "julia --project -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
- "julia --project -e 'using Pkg; Pkg.precompile()'"
- "julia --project -e 'using Pkg; Pkg.status()'"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "init gpu env"
key: "init_gpu_env"
command:
- "echo $JULIA_DEPOT_PATH"
- "julia --project -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
- "julia --project -e 'using Pkg; Pkg.precompile()'"
# force the initialization of the CUDA runtime
# as it is lazily loaded by default
- "julia --project -e 'using CUDA; CUDA.versioninfo()'"
# force the initialization of the CUDA Compiler runtime
# as it is lazily generated by default
- "julia --project -e 'using CUDA; CUDA.precompile_runtime()'"
- "julia --project -e 'using Pkg; Pkg.status()'"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- wait
- label: "cpu_advection_diffusion_model_1dimex_bgmres"
key: "cpu_advection_diffusion_model_1dimex_bgmres"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/advection_diffusion_model_1dimex_bgmres.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_fvm_advection_diffusion_model_1dimex_bjfnks"
key: "cpu_fvm_advection_diffusion_model_1dimex_bjfnks"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_advection_diffusion_model_1dimex_bjfnks.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_pseudo1D_advection_diffusion"
key: "cpu_pseudo1D_advection_diffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/pseudo1D_advection_diffusion.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_pseudo1D_advection_diffusion_1dimex"
key: "cpu_pseudo1D_advection_diffusion_1dimex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/pseudo1D_advection_diffusion_1dimex.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_pseudo1D_advection_diffusion_mrigark_implicit"
key: "cpu_pseudo1D_advection_diffusion_mrigark_implicit"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/pseudo1D_advection_diffusion_mrigark_implicit.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_pseudo1D_heat_eqn"
key: "cpu_pseudo1D_heat_eqn"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/pseudo1D_heat_eqn.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_bickley_jet_2D"
key: "cpu_bickley_jet_2D"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_navier_stokes_equations/two_dimensional/test_bickley_jet.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_periodic_3D_hyperdiffusion"
key: "cpu_periodic_3D_hyperdiffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/periodic_3D_hyperdiffusion.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_hyperdiffusion_bc"
key: "cpu_hyperdiffusion_bc"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/hyperdiffusion_bc.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_diffusion_hyperdiffusion_sphere"
key: "cpu_diffusion_hyperdiffusion_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/diffusion_hyperdiffusion_sphere.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_mpi_connect_1d"
key: "cpu_mpi_connect_1d"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_connect_1d.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 5
- label: "cpu_mpi_connect_sphere"
key: "cpu_mpi_connect_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_connect_sphere.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 5
- label: "cpu_mpi_getpartition"
key: "cpu_mpi_getpartition"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_getpartition.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 5
- label: "cpu_mpi_sortcolumns4"
key: "cpu_mpi_sortcolumns4"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_sortcolumns.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 4
- label: "cpu_ode_tests_convergence"
key: "cpu_ode_tests_convergence"
command:
- "mpiexec julia --color=yes --project test/Numerics/ODESolvers/ode_tests_convergence.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_ode_tests_basic"
key: "cpu_ode_tests_basic"
command:
- "mpiexec julia --color=yes --project test/Numerics/ODESolvers/ode_tests_basic.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_varsindex"
key: "cpu_varsindex"
command:
- "mpiexec julia --color=yes --project test/Arrays/varsindex.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_diagnostic_fields_test"
key: "cpu_diagnostic_fields_test"
command:
- "mpiexec julia --color=yes --project test/Diagnostics/diagnostic_fields_test.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_vars_test"
key: "cpu_vars_test"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/vars_test.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_grad_test"
key: "cpu_grad_test"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/grad_test.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_grad_test_sphere"
key: "cpu_grad_test_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/grad_test_sphere.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_horizontal_integral_test"
key: "cpu_horizontal_integral_test"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/horizontal_integral_test.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_integral_test"
key: "cpu_integral_test"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/integral_test.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_integral_test_sphere"
key: "cpu_integral_test_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/integral_test_sphere.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_custom_filter"
key: "cpu_custom_filter"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/custom_filter.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_fv_reconstruction_test"
key: "cpu_fv_reconstruction_test"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/fv_reconstruction_test.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_remainder_model"
key: "cpu_remainder_model"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/remainder_model.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_isentropicvortex"
key: "cpu_isentropicvortex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_isentropicvortex_imex"
key: "cpu_isentropicvortex_imex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_imex.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_isentropicvortex_lmars"
key: "cpu_isentropicvortex_lmars"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_lmars.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_isentropicvortex_multirate"
key: "cpu_isentropicvortex_multirate"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_multirate.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_isentropicvortex_mrigark"
key: "cpu_isentropicvortex_mrigark"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_mrigark.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_isentropicvortex_mrigark_implicit"
key: "cpu_isentropicvortex_mrigark_implicit"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_mrigark_implicit.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_acousticwave_1d_imex"
key: "cpu_acousticwave_1d_imex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/acousticwave_1d_imex.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_acousticwave_mrigark"
key: "cpu_acousticwave_mrigark"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/acousticwave_mrigark.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_acousticwave_variable_degree"
key: "cpu_acousticwave_variable_degree"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/acousticwave_variable_degree.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_fvm_balance"
key: "cpu_fvm_balance"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/fvm_balance.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_mms_bc_atmos"
key: "cpu_mms_bc_atmos"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_Navier_Stokes/mms_bc_atmos.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_mms_bc_dgmodel"
key: "cpu_mms_bc_dgmodel"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_Navier_Stokes/mms_bc_dgmodel.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_density_current_model"
key: "cpu_density_current_model"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_Navier_Stokes/density_current_model.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_direction_splitting_advection_diffusion"
key: "cpu_direction_splitting_advection_diffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/direction_splitting_advection_diffusion.jl --fix-rng-seed"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_variable_degree_advection_diffusion"
key: "cpu_variable_degree_advection_diffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/variable_degree_advection_diffusion.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_sphere"
key: "cpu_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/conservation/sphere.jl --fix-rng-seed"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_advection_sphere"
key: "cpu_advection_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/advection_sphere.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_fvm_advection_sphere"
key: "cpu_fvm_advection_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_advection_sphere.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_fvm_swirl"
key: "cpu_fvm_swirl"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_swirl.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_fvm_advection"
key: "cpu_fvm_advection"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_advection.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_fvm_advection_diffusion"
key: "cpu_fvm_advection_diffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_advection_diffusion.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_fvm_advection_diffusion_periodic"
key: "cpu_fvm_advection_diffusion_periodic"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_advection_diffusion_periodic.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_fvm_isentropicvortex"
key: "cpu_fvm_isentropicvortex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/fvm_isentropicvortex.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_gcm_driver_test"
key: "cpu_gcm_driver_test"
command:
- "mpiexec julia --color=yes --project test/Driver/gcm_driver_test.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_poisson"
key: "cpu_poisson"
command:
- "mpiexec julia --color=yes --project test/Numerics/SystemSolvers/poisson.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_columnwiselu"
key: "cpu_columnwiselu"
command:
- "mpiexec julia --color=yes --project test/Numerics/SystemSolvers/columnwiselu.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_cg"
key: "cpu_cg"
command:
- "mpiexec julia --color=yes --project test/Numerics/SystemSolvers/cg.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_bgmres"
key: "cpu_bgmres"
command:
- "mpiexec julia --color=yes --project test/Numerics/SystemSolvers/bgmres.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_bandedsystem"
key: "cpu_bandedsystem"
command:
- "mpiexec julia --color=yes --project test/Numerics/SystemSolvers/bandedsystem.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_interpolation"
key: "cpu_interpolation"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/interpolation.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_dss_mpi"
key: "cpu_dss_mpi"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/DSS_mpi.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_dss"
key: "cpu_dss"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/DSS.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_GyreDriver"
key: "cpu_GyreDriver"
command:
- "mpiexec julia --color=yes --project test/Ocean/ShallowWater/GyreDriver.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_test_windstress_short"
key: "cpu_test_windstress_short"
command:
- "mpiexec julia --color=yes --project test/Ocean/HydrostaticBoussinesq/test_windstress_short.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_test_ocean_gyre_short"
key: "cpu_test_ocean_gyre_short"
command:
- "mpiexec julia --color=yes --project test/Ocean/HydrostaticBoussinesq/test_ocean_gyre_short.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_test_2D_spindown"
key: "cpu_test_2D_spindown"
command:
- "mpiexec julia --color=yes --project test/Ocean/ShallowWater/test_2D_spindown.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_test_3D_spindown"
key: "cpu_test_3D_spindown"
command:
- "mpiexec julia --color=yes --project test/Ocean/HydrostaticBoussinesq/test_3D_spindown.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_test_vertical_integral_model"
key: "cpu_test_vertical_integral_model"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/test_vertical_integral_model.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_test_spindown_long"
key: "cpu_test_spindown_long"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/test_spindown_long.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_test_restart"
key: "cpu_test_restart"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/test_restart.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_test_coriolis"
key: "cpu_test_coriolis"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/test_coriolis.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_KM_saturation_adjustment"
key: "cpu_KM_saturation_adjustment"
command:
- "mpiexec julia --color=yes --project test/Atmos/Parameterizations/Microphysics/KM_saturation_adjustment.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_KM_warm_rain"
key: "cpu_KM_warm_rain"
command:
- "mpiexec julia --color=yes --project test/Atmos/Parameterizations/Microphysics/KM_warm_rain.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_haverkamp_test"
key: "cpu_haverkamp_test"
command:
- "mpiexec julia --color=yes --project test/Land/Model/haverkamp_test.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_soil_params"
key: "cpu_soil_params"
command:
- "mpiexec julia --color=yes --project test/Land/Model/soil_heterogeneity.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_heat_analytic_unit_test"
key: "cpu_heat_analytic_unit_test"
command:
- "mpiexec julia --color=yes --project test/Land/Model/heat_analytic_unit_test.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_discrete_hydrostatic_balance"
key: "cpu_discrete_hydrostatic_balance"
command:
- "mpiexec julia --color=yes --project test/Atmos/Model/discrete_hydrostatic_balance.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_soil_test_bc"
key: "cpu_soil_test_bc"
command:
- "mpiexec julia --color=yes --project test/Land/Model/test_bc.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_soil_test_bc_3d"
key: "cpu_soil_test_bc_3d"
command:
- "mpiexec julia --color=yes --project test/Land/Model/test_bc_3d.jl "
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "gpu_varsindex"
key: "gpu_varsindex"
command:
- "mpiexec julia --color=yes --project test/Arrays/varsindex.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_variable_templates"
key: "gpu_variable_templates"
command:
- "mpiexec julia --color=yes --project test/Utilities/VariableTemplates/runtests_gpu.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "cpu_land_overland_flow_vcatchment"
key: "cpu_land_overland_flow_vcatchment"
command:
- "mpiexec julia --color=yes --project test/Land/Model/test_overland_flow_vcatchment.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "gpu_diagnostic_fields_test"
key: "gpu_diagnostic_fields_test"
command:
- "mpiexec julia --color=yes --project test/Diagnostics/diagnostic_fields_test.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_vars_test"
key: "gpu_vars_test"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/vars_test.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_custom_filter"
key: "gpu_custom_filter"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/custom_filter.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_remainder_model"
key: "gpu_remainder_model"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/remainder_model.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 2
slurm_gres: "gpu:1"
- label: "gpu_isentropicvortex"
key: "gpu_isentropicvortex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_isentropicvortex_imex"
key: "gpu_isentropicvortex_imex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_imex.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_isentropicvortex_lmars"
key: "gpu_isentropicvortex_lmars"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_lmars.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_isentropicvortex_multirate"
key: "gpu_isentropicvortex_multirate"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_multirate.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_isentropicvortex_mrigark"
key: "gpu_isentropicvortex_mrigark"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_mrigark.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_isentropicvortex_mrigark_implicit"
key: "gpu_isentropicvortex_mrigark_implicit"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/isentropicvortex_mrigark_implicit.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_acousticwave_1d_imex"
key: "gpu_acousticwave_1d_imex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/acousticwave_1d_imex.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_acousticwave_mrigark"
key: "gpu_acousticwave_mrigark"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/acousticwave_mrigark.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_acousticwave_variable_degree"
key: "gpu_acousticwave_variable_degree"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/acousticwave_variable_degree.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_fvm_balance"
key: "gpu_fvm_balance"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/fvm_balance.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_mms_bc_atmos"
key: "gpu_mms_bc_atmos"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_Navier_Stokes/mms_bc_atmos.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_mms_bc_dgmodel"
key: "gpu_mms_bc_dgmodel"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_Navier_Stokes/mms_bc_dgmodel.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_density_current_model"
key: "gpu_density_current_model"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_Navier_Stokes/density_current_model.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_direction_splitting_advection_diffusion"
key: "gpu_direction_splitting_advection_diffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/direction_splitting_advection_diffusion.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_variable_degree_advection_diffusion"
key: "gpu_variable_degree_advection_diffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/variable_degree_advection_diffusion.jl"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_sphere"
key: "gpu_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/conservation/sphere.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_advection_sphere"
key: "gpu_advection_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/advection_sphere.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 2
slurm_gres: "gpu:1"
- label: "gpu_fvm_advection_sphere"
key: "gpu_fvm_advection_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_advection_sphere.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 2
slurm_gres: "gpu:1"
- label: "gpu_fvm_swirl"
key: "gpu_fvm_swirl"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_swirl.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 2
slurm_gres: "gpu:1"
- label: "gpu_fvm_advection"
key: "gpu_fvm_advection"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_advection.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 2
slurm_gres: "gpu:1"
- label: "gpu_fvm_advection_diffusion"
key: "gpu_fvm_advection_diffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_advection_diffusion.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 2
slurm_gres: "gpu:1"
- label: "gpu_fvm_advection_diffusion_periodic"
key: "gpu_fvm_advection_diffusion_periodic"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/fvm_advection_diffusion_periodic.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 2
slurm_gres: "gpu:1"
- label: "gpu_fvm_isentropicvortex"
key: "gpu_fvm_isentropicvortex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/Euler/fvm_isentropicvortex.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 2
slurm_gres: "gpu:1"
- label: "gpu_gcm_driver_test"
key: "gpu_gcm_driver_test"
command:
- "mpiexec julia --color=yes --project test/Driver/gcm_driver_test.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_poisson"
key: "gpu_poisson"
command:
- "mpiexec julia --color=yes --project test/Numerics/SystemSolvers/poisson.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 2
slurm_gres: "gpu:1"
- label: "gpu_columnwiselu"
key: "gpu_columnwiselu"
command:
- "mpiexec julia --color=yes --project test/Numerics/SystemSolvers/columnwiselu.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_bandedsystem"
key: "gpu_bandedsystem"
command:
- "mpiexec julia --color=yes --project test/Numerics/SystemSolvers/bandedsystem.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "cpu_courant"
key: "cpu_courant"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/courant.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_brickmesh"
key: "cpu_brickmesh"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/BrickMesh.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_elements"
key: "cpu_elements"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/Elements.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_metrics"
key: "cpu_metrics"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/Metrics.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_grids"
key: "cpu_grids"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/Grids.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_topology"
key: "cpu_topology"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/topology.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_grid_integral"
key: "cpu_grid_integral"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/grid_integral.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_filter"
key: "cpu_filter"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/filter.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_filter_tmar"
key: "cpu_filter_tmar"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/filter_TMAR.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "cpu_mpi_centroid"
key: "cpu_mpi_centroid"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_centroid.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_mpi_connect_ell"
key: "cpu_mpi_connect_ell"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_connect_ell.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_mpi_connect"
key: "cpu_mpi_connect"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_connect.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_mpi_connectfull"
key: "cpu_mpi_connectfull"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_connectfull.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_mpi_connect_stacked"
key: "cpu_mpi_connect_stacked"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_connect_stacked.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_mpi_connect_stacked_3d"
key: "cpu_mpi_connect_stacked_3d"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_connect_stacked_3d.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 2
- label: "cpu_mpi_getpartition3"
key: "cpu_mpi_getpartition3"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_getpartition.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_mpi_partition"
key: "cpu_mpi_partition"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_partition.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 3
- label: "cpu_mpi_sortcolumns"
key: "cpu_mpi_sortcolumns"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/mpi_sortcolumns.jl"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "gpu_interpolation"
key: "gpu_interpolation"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/interpolation.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_dss_mpi"
key: "gpu_dss_mpi"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/DSS_mpi.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_dss"
key: "gpu_dss"
command:
- "mpiexec julia --color=yes --project test/Numerics/Mesh/DSS.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_GyreDriver"
key: "gpu_GyreDriver"
command:
- "mpiexec julia --color=yes --project test/Ocean/ShallowWater/GyreDriver.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_test_windstress_short"
key: "gpu_test_windstress_short"
command:
- "mpiexec julia --color=yes --project test/Ocean/HydrostaticBoussinesq/test_windstress_short.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_test_ocean_gyre_short"
key: "gpu_test_ocean_gyre_short"
command:
- "mpiexec julia --color=yes --project test/Ocean/HydrostaticBoussinesq/test_ocean_gyre_short.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_test_2D_spindown"
key: "gpu_test_2D_spindown"
command:
- "mpiexec julia --color=yes --project test/Ocean/ShallowWater/test_2D_spindown.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_test_3D_spindown"
key: "gpu_test_3D_spindown"
command:
- "mpiexec julia --color=yes --project test/Ocean/HydrostaticBoussinesq/test_3D_spindown.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_test_vertical_integral_model"
key: "gpu_test_vertical_integral_model"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/test_vertical_integral_model.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_test_spindown_long"
key: "gpu_test_spindown_long"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/test_spindown_long.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_test_restart"
key: "gpu_test_restart"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/test_restart.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_test_coriolis"
key: "gpu_test_coriolis"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/test_coriolis.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_KM_saturation_adjustment"
key: "gpu_KM_saturation_adjustment"
command:
- "mpiexec julia --color=yes --project test/Atmos/Parameterizations/Microphysics/KM_saturation_adjustment.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_KM_warm_rain"
key: "gpu_KM_warm_rain"
command:
- "mpiexec julia --color=yes --project test/Atmos/Parameterizations/Microphysics/KM_warm_rain.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_KM_ice"
key: "gpu_KM_ice"
command:
- "mpiexec julia --color=yes --project test/Atmos/Parameterizations/Microphysics/KM_ice.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_pseudo1D_advection_diffusion"
key: "gpu_pseudo1D_advection_diffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/pseudo1D_advection_diffusion.jl --integration-testing"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_pseudo1D_advection_diffusion_1dimex"
key: "gpu_pseudo1D_advection_diffusion_1dimex"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/pseudo1D_advection_diffusion_1dimex.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_pseudo1D_advection_diffusion_mrigark_implicit"
key: "gpu_pseudo1D_advection_diffusion_mrigark_implicit"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/pseudo1D_advection_diffusion_mrigark_implicit.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_pseudo1D_heat_eqn"
key: "gpu_pseudo1D_heat_eqn"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/pseudo1D_heat_eqn.jl --integration-testing"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_bickley_jet_2D"
key: "gpu_bickley_jet_2D"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_navier_stokes_equations/two_dimensional/test_bickley_jet.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_bickley_jet_3D"
key: "gpu_bickley_jet_3D"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_navier_stokes_equations/three_dimensional/test_bickley_jet.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_cnse_buoyancy_3D"
key: "gpu_cnse_buoyancy_3D"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_navier_stokes_equations/three_dimensional/test_buoyancy.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_cnse_sphere_3D"
key: "gpu_cnse_sphere_3D"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_navier_stokes_equations/sphere/test_sphere.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_cnse_sphere_heat_3D"
key: "gpu_cnse_sphere_heat_3D"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_navier_stokes_equations/sphere/test_heat_equation.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_cnse_sphere_balance_3D"
key: "gpu_cnse_sphere_balance_3D"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/compressible_navier_stokes_equations/sphere/test_hydrostatic_balance.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_periodic_3D_hyperdiffusion"
key: "gpu_periodic_3D_hyperdiffusion"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/periodic_3D_hyperdiffusion.jl --integration-testing"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_hyperdiffusion_bc"
key: "gpu_hyperdiffusion_bc"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/hyperdiffusion_bc.jl --integration-testing"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_diffusion_hyperdiffusion_sphere"
key: "gpu_diffusion_hyperdiffusion_sphere"
command:
- "mpiexec julia --color=yes --project test/Numerics/DGMethods/advection_diffusion/diffusion_hyperdiffusion_sphere.jl --integration-testing"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_esdg_baroclinic_wave"
key: "gpu_esdg_baroclinic_wave"
command:
- "mpiexec julia --color=yes --project test/Numerics/ESDGMethods/DryAtmos/baroclinic_wave.jl"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_dry_rayleigh_benard"
key: "gpu_dry_rayleigh_benard"
command:
- "mpiexec julia --color=yes --project tutorials/Atmos/dry_rayleigh_benard.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_dry_risingbubble"
key: "gpu_dry_risingbubble"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/risingbubble.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_dry_risingbubble_fvm"
key: "gpu_dry_risingbubble_fvm"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/risingbubble_fvm.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_moist_risingbubble"
key: "gpu_moist_risingbubble"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/risingbubble.jl --with-moisture "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_solid_body_rotation"
key: "gpu_solid_body_rotation"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/solid_body_rotation.jl --diagnostics=default "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_solid_body_rotation_fvm"
key: "gpu_solid_body_rotation_fvm"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/solid_body_rotation_fvm.jl --diagnostics=default "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_solid_body_rotation_mountain"
key: "gpu_solid_body_rotation_mountain"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/solid_body_rotation_mountain.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_dry_baroclinic_wave"
key: "gpu_dry_baroclinic_wave"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/baroclinic_wave.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_dry_baroclinic_wave_fvm"
key: "gpu_dry_baroclinic_wave_fvm"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/baroclinic_wave_fvm.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_moist_baroclinic_wave"
key: "gpu_moist_baroclinic_wave"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/baroclinic_wave.jl --with-moisture "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_heldsuarez"
key: "gpu_heldsuarez"
command:
- "mpiexec julia --color=yes --project experiments/AtmosGCM/heldsuarez.jl --diagnostics=default --fix-rng-seed "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_nonhydrostatic_gravity_wave"
key: "gpu_nonhydrostatic_gravity_wave"
command:
- "mpiexec julia --color=yes --project experiments/AtmosGCM/nonhydrostatic_gravity_wave.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_isothermal_zonal_flow"
key: "gpu_isothermal_zonal_flow"
command:
- "mpiexec julia --color=yes --project experiments/TestCase/isothermal_zonal_flow.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_surfacebubble"
key: "gpu_surfacebubble"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/surfacebubble.jl --diagnostics=default"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_dycoms"
key: "gpu_dycoms"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/dycoms.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_dycoms_with_precip"
key: "gpu_dycoms_with_precip"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/dycoms.jl --fix-rng-seed --moisture-model nonequilibrium --precipitation-model rain --sim-time 120 --check-asserts yes"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_squall_eq_no_precip"
key: "gpu_squall_eq_no_precip"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/squall_line.jl --fix-rng-seed --sim-time 600 --check-asserts yes --moisture-model equilibrium --precipitation-model noprecipitation"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_squall_eq_rain"
key: "gpu_squall_eq_rain"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/squall_line.jl --fix-rng-seed --sim-time 600 --check-asserts yes --moisture-model equilibrium --precipitation-model rain"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_squall_neq_rain_snow"
key: "gpu_squall_neq_rain_snow"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/squall_line.jl --fix-rng-seed --sim-time 600 --check-asserts yes --moisture-model nonequilibrium --precipitation-model rainsnow"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_bomex_les"
key: "gpu_bomex_les"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/bomex_les.jl --diagnostics=default --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_sbl_les"
key: "gpu_sbl_les"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/stable_bl_les.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_cbl_les"
key: "gpu_cbl_les"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/convective_bl_les.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_cfsite"
key: "gpu_cfsite"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/cfsite_hadgem2-a_07_amip.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_bomex_single_stack"
key: "gpu_bomex_single_stack"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/bomex_single_stack.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_bomex_single_stack_nonequil"
key: "gpu_bomex_single_stack_nonequil"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/bomex_single_stack.jl --moisture-model nonequilibrium --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_bomex_edmf"
key: "gpu_bomex_edmf"
command:
- "mpiexec julia --color=yes --project test/Atmos/EDMF/bomex_edmf.jl --diagnostics=default --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_ekman"
key: "gpu_ekman"
command:
- "mpiexec julia --color=yes --project test/Atmos/EDMF/ekman_layer.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_sbl_edmf"
key: "gpu_sbl_edmf"
command:
- "mpiexec julia --color=yes --project test/Atmos/EDMF/stable_bl_edmf.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "cpu_sbl_edmf_fvm"
key: "cpu_sbl_edmf_fvm"
command:
- "mpiexec julia --color=yes --project test/Atmos/EDMF/stable_bl_edmf_fvm.jl --fix-rng-seed"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "gpu_sbl_an1d"
key: "gpu_sbl_an1d"
command:
- "mpiexec julia --color=yes --project test/Atmos/EDMF/stable_bl_anelastic1d.jl --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "cpu_sbl_edmf_coupled"
key: "cpu_sbl_edmf_coupled"
command:
- "mpiexec julia --color=yes --project test/Atmos/EDMF/stable_bl_coupled_edmf_an1d.jl --fix-rng-seed"
agents:
config: cpu
queue: central
slurm_ntasks: 1
- label: "gpu_bomex_bulk_sfc_flux"
key: "gpu_bomex_bulk_sfc_flux"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/bomex_les.jl --surface-flux=bulk --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_taylor_green"
key: "gpu_taylor_green"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/taylor_green.jl --diagnostics=default --fix-rng-seed"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_rising_bubble_theta_formulation"
key: "gpu_rising_bubble_theta_formulation"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/rising_bubble_theta_formulation.jl"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_rising_bubble_bryan_mrrk"
key: "gpu_rising_bubble_bryan_mrrk"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/rising_bubble_bryan.jl --fast-method=MultirateRungeKutta "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_rising_bubble_bryan_ark"
key: "gpu_rising_bubble_bryan_ark"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/rising_bubble_bryan.jl --fast-method=AdditiveRungeKutta "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_rising_bubble_bryan_mis"
key: "gpu_rising_bubble_bryan_mis"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/rising_bubble_bryan.jl --fast-method=MultirateInfinitesimalStep "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_schar_scalar_advection"
key: "gpu_schar_scalar_advection"
command:
- "mpiexec julia --color=yes --project experiments/AtmosLES/schar_scalar_advection.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_test_windstress_long"
key: "gpu_test_windstress_long"
command:
- "mpiexec julia --color=yes --project test/Ocean/HydrostaticBoussinesq/test_windstress_long.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_test_ocean_gyre_long"
key: "gpu_test_ocean_gyre_long"
command:
- "mpiexec julia --color=yes --project test/Ocean/HydrostaticBoussinesq/test_ocean_gyre_long.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_simple_box_ivd"
key: "gpu_simple_box_ivd"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/simple_box_ivd.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_simple_dbl_gyre"
key: "gpu_simple_dbl_gyre"
command:
- "mpiexec julia --color=yes --project test/Ocean/SplitExplicit/simple_dbl_gyre.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_discrete_hydrostatic_balance"
key: "gpu_discrete_hydrostatic_balance"
command:
- "mpiexec julia --color=yes --project test/Atmos/Model/discrete_hydrostatic_balance.jl"
agents:
config: gpu
queue: central
slurm_ntasks: 3
slurm_gres: "gpu:1"
- label: "gpu_haverkamp_test"
key: "gpu_haverkamp_test"
command:
- "mpiexec julia --color=yes --project test/Land/Model/haverkamp_test.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_soil_params"
key: "gpu_soil_params"
command:
- "mpiexec julia --color=yes --project test/Land/Model/soil_heterogeneity.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_stable_bl_edmf_implicit_test"
key: "gpu_stable_bl_edmf_implicit_test"
command:
- "mpiexec julia --color=yes --project test/Atmos/EDMF/stable_bl_single_stack_implicit.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_heat_analytic_unit_test"
key: "gpu_heat_analytic_unit_test"
command:
- "mpiexec julia --color=yes --project test/Land/Model/heat_analytic_unit_test.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_soil_test_bc"
key: "gpu_soil_test_bc"
command:
- "mpiexec julia --color=yes --project test/Land/Model/test_bc.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_soil_test_bc_3d"
key: "gpu_soil_test_bc_3d"
command:
- "mpiexec julia --color=yes --project test/Land/Model/test_bc_3d.jl "
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_land_overland_flow_vcatchment"
key: "gpu_land_overland_flow_vcatchment"
command:
- "mpiexec julia --color=yes --project test/Land/Model/test_overland_flow_vcatchment.jl"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
- label: "gpu_unittests"
key: "gpu_unittests"
command:
- "julia --color=yes --project test/runtests_gpu.jl"
agents:
config: gpu
queue: central
slurm_ntasks: 1
slurm_gres: "gpu:1"
================================================
FILE: .codecov.yml
================================================
comment: off
================================================
FILE: .dev/.gitignore
================================================
Manifest.toml
================================================
FILE: .dev/Project.toml
================================================
[deps]
JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
[compat]
JuliaFormatter = "0.10"
================================================
FILE: .dev/clima_formatter_default_image.jl
================================================
#!/usr/bin/env julia
#! format: off
#
# Called with no arguments will replace the default system image with one that
# includes the JuliaFormatter
#
# Called with a single argument the system image for the formatter will be
# placed in the path specified by the argument (relative to the callers path)
using Pkg
Pkg.add("PackageCompiler")
using PackageCompiler
if isfile(PackageCompiler.backup_default_sysimg_path())
@error """
A custom default system image already exists.
Either restore default with:
julia -e "using PackageCompiler; PackageCompiler.restore_default_sysimage()"
or use the script
$(abspath(joinpath(@__DIR__, "..", ".dev", "clima_formatter_image.jl")))
which will use a custom path for the system image
"""
exit(1)
end
# If a current Manifest exist for the formatter we remove it so that we have the
# latest version
rm(joinpath(@__DIR__, "Manifest.toml"); force = true)
Pkg.activate(joinpath(@__DIR__))
PackageCompiler.create_sysimage(
:JuliaFormatter;
precompile_execution_file = joinpath(@__DIR__, "precompile.jl"),
replace_default = true,
)
================================================
FILE: .dev/clima_formatter_image.jl
================================================
#!/usr/bin/env julia
#
# Called with no arguments will build the formattter system image
# PATH_TO_CLIMATEMACHINE/.git/hooks/JuliaFormatterSysimage.so
#
# Called with a single argument the system image for the formatter will be
# placed in the path specified by the argument (relative to the callers path)
sysimage_path = abspath(
isempty(ARGS) ?
joinpath(@__DIR__, "..", ".git", "hooks", "JuliaFormatterSysimage.so") :
ARGS[1],
)
@info """
Creating system image object file at:
$(sysimage_path)
"""
using Pkg
Pkg.add("PackageCompiler")
using PackageCompiler
# If a current Manifest exist for the formatter we remove it so that we have the
# latest version
rm(joinpath(@__DIR__, "Manifest.toml"); force = true)
Pkg.activate(joinpath(@__DIR__))
PackageCompiler.create_sysimage(
:JuliaFormatter;
precompile_execution_file = joinpath(@__DIR__, "precompile.jl"),
sysimage_path = sysimage_path,
)
================================================
FILE: .dev/clima_formatter_options.jl
================================================
clima_formatter_options = (
indent = 4,
margin = 80,
always_for_in = true,
whitespace_typedefs = true,
whitespace_ops_in_indices = true,
remove_extra_newlines = false,
)
================================================
FILE: .dev/climaformat.jl
================================================
#!/usr/bin/env julia
#
# This is an adapted version of format.jl from JuliaFormatter with the
# following license:
#
# MIT License
# Copyright (c) 2019 Dominique Luna
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to permit
# persons to whom the Software is furnished to do so, subject to the
# following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
# NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
# USE OR OTHER DEALINGS IN THE SOFTWARE.
#
using Pkg
Pkg.activate(@__DIR__)
Pkg.instantiate()
using JuliaFormatter
include("clima_formatter_options.jl")
help = """
Usage: climaformat.jl [flags] [FILE/PATH]...
Formats the given julia files using the CLIMA formatting options. If paths
are given it will format the julia files in the paths. Otherwise, it will
format all changed julia files.
-v, --verbose
Print the name of the files being formatted with relevant details.
-h, --help
Print this message.
"""
function parse_opts!(args::Vector{String})
i = 1
opts = Dict{Symbol, Union{Int, Bool}}()
while i ≤ length(args)
arg = args[i]
if arg[1] != '-'
i += 1
continue
end
if arg == "-v" || arg == "--verbose"
opt = :verbose
elseif arg == "-h" || arg == "--help"
opt = :help
else
error("invalid option $arg")
end
if opt in (:verbose, :help)
opts[opt] = true
deleteat!(args, i)
end
end
return opts
end
opts = parse_opts!(ARGS)
if haskey(opts, :help)
write(stdout, help)
exit(0)
end
if isempty(ARGS)
filenames = readlines(`git ls-files "*.jl"`)
else
filenames = ARGS
end
format(filenames; clima_formatter_options..., opts...)
================================================
FILE: .dev/hooks/pre-commit
================================================
#!/usr/bin/env julia
#
# Called by git-commit with no arguments. This checks to make sure that all
# .jl files are indented correctly before a commit is made.
#
# To enable this hook, make this file executable and copy it in
# $GIT_DIR/hooks.
toplevel_directory = chomp(read(`git rev-parse --show-toplevel`, String))
using Pkg
Pkg.activate(joinpath(toplevel_directory, ".dev"))
Pkg.instantiate()
using JuliaFormatter
include(joinpath(toplevel_directory, ".dev", "clima_formatter_options.jl"))
needs_format = false
for diffoutput in split.(readlines(`git diff --name-status --cached`))
status = diffoutput[1]
filename = diffoutput[end]
(!startswith(status, "D") && endswith(filename, ".jl")) || continue
a = read(`git show :$filename`, String)
b = format_text(a; clima_formatter_options...)
if a != b
fullfilename = joinpath(toplevel_directory, filename)
@error """File $filename needs to be indented with:
julia $(joinpath(toplevel_directory, ".dev", "climaformat.jl")) $fullfilename
and added to the git index via
git add $fullfilename
"""
global needs_format = true
end
end
exit(needs_format ? 1 : 0)
================================================
FILE: .dev/hooks/pre-commit.sysimage
================================================
#!/usr/bin/env -S julia -J.git/hooks/JuliaFormatterSysimage.so
#
# Called by git-commit with no arguments. This checks to make sure that all
# .jl files are indented correctly before a commit is made.
#
# To enable this hook, make this file executable and copy it in
# $GIT_DIR/hooks.
toplevel_directory = chomp(read(`git rev-parse --show-toplevel`, String))
using Pkg
Pkg.activate(joinpath(toplevel_directory, ".dev"))
Pkg.instantiate()
using JuliaFormatter
include(joinpath(toplevel_directory, ".dev", "clima_formatter_options.jl"))
needs_format = false
for diffoutput in split.(readlines(`git diff --name-status --cached`))
status = diffoutput[1]
filename = diffoutput[end]
(!startswith(status, "D") && endswith(filename, ".jl")) || continue
a = read(`git show :$filename`, String)
b = format_text(a; clima_formatter_options...)
if a != b
fullfilename = joinpath(toplevel_directory, filename)
@error """File $filename needs to be indented with:
julia -J$(joinpath(toplevel_directory, ".git/hooks", "JuliaFormatterSysimage.so")) $(joinpath(toplevel_directory, ".dev", "climaformat.jl")) $fullfilename
and added to the git index via
git add $fullfilename
"""
global needs_format = true
end
end
exit(needs_format ? 1 : 0)
================================================
FILE: .dev/precompile.jl
================================================
using JuliaFormatter
include("clima_formatter_options.jl")
format(@__FILE__; clima_formatter_options...)
================================================
FILE: .dev/systemimage/climate_machine_image.jl
================================================
#!/usr/bin/env julia
#
# Called with no arguments will create the system image
# ClimateMachine.so
# in the `@__DIR__` directory.
#
# Called with a single argument the system image will be placed in the path
# specified by the argument (relative to the callers path)
#
# Called with a specified systemimg path and `true`, the system image will
# compile the climate machine package module (useful for CI)
sysimage_path =
isempty(ARGS) ? joinpath(@__DIR__, "ClimateMachine.so") : abspath(ARGS[1])
climatemachine_pkg = get(ARGS, 2, "false") == "true"
@info "Creating system image object file at: '$(sysimage_path)'"
@info "Building ClimateMachine into system image: $(climatemachine_pkg)"
start_time = time()
using Pkg
Pkg.add("PackageCompiler")
Pkg.activate(joinpath(@__DIR__, "..", ".."))
Pkg.instantiate(verbose = true)
pkgs = Symbol[]
if climatemachine_pkg
push!(pkgs, :ClimateMachine)
else
append!(
pkgs,
[Symbol(v.name) for v in values(Pkg.dependencies()) if v.is_direct_dep],
)
end
# use package compiler
using PackageCompiler
PackageCompiler.create_sysimage(
pkgs,
sysimage_path = sysimage_path,
precompile_execution_file = joinpath(
@__DIR__,
"..",
"..",
"test",
"Numerics",
"DGMethods",
"Euler",
"isentropicvortex.jl",
),
)
tot_secs = Int(floor(time() - start_time))
@info "Created system image object file at: $(sysimage_path)"
@info "System image build time: $tot_secs sec"
================================================
FILE: .github/issue_template.md
================================================
### Description
<!-- Provide a clear description of the issue including any relevant logs or screenshots. Add `bug`, `enhancement` or other labels as appropriate. -->
================================================
FILE: .github/pull_request_template.md
================================================
### Description
<!-- Provide a clear description of the content -->
<!-- Check all the boxes below before taking the PR out of draft -->
- [ ] Code follows the [style guidelines](https://clima.github.io/ClimateMachine.jl/latest/DevDocs/CodeStyle/) OR N/A.
- [ ] Unit tests are included OR N/A.
- [ ] Code is exercised in an integration test OR N/A.
- [ ] Documentation has been added/updated OR N/A.
================================================
FILE: .github/workflows/CompatHelper.yml
================================================
name: CompatHelper
on:
schedule:
- cron: '00 * * * *'
jobs:
CompatHelper:
runs-on: ubuntu-latest
steps:
- uses: julia-actions/setup-julia@latest
with:
version: 1.5.4
- name: Pkg.add("CompatHelper")
run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
- name: CompatHelper.main()
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: julia -e 'using CompatHelper; CompatHelper.main()'
================================================
FILE: .github/workflows/Coverage.yaml
================================================
name: Coverage
on:
schedule:
# * is a special character in YAML so you have to quote this string
# Run at 2am every day:
- cron: '0 2 * * *'
jobs:
coverage:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2.2.0
- name: Set up Julia
uses: julia-actions/setup-julia@latest
with:
version: 1.5.4
- name: Test with coverage
run: |
julia --project -e 'using Pkg; Pkg.instantiate()'
julia --project -e 'using Pkg; Pkg.test(coverage=true)'
- name: Generate coverage file
run: julia --project -e 'using Pkg; Pkg.add("Coverage");
using Coverage;
LCOV.writefile("coverage-lcov.info", Codecov.process_folder())'
if: success()
- name: Submit coverage
uses: codecov/codecov-action@v1.0.7
with:
token: ${{secrets.CODECOV_TOKEN}}
if: success()
================================================
FILE: .github/workflows/DocCleanup.yml
================================================
name: Doc Preview Cleanup
on:
pull_request:
types: [closed]
jobs:
doc-preview-cleanup:
runs-on: ubuntu-latest
steps:
- name: Checkout gh-pages branch
uses: actions/checkout@v2
with:
ref: gh-pages
- name: Delete preview and history
run: |
git config user.name "Documenter.jl"
git config user.email "documenter@juliadocs.github.io"
git rm -rf "previews/PR$PRNUM"
git commit -m "delete preview"
git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
env:
PRNUM: ${{ github.event.number }}
- name: Push changes
run: |
git push --force origin gh-pages-new:gh-pages
================================================
FILE: .github/workflows/Documenter.yaml
================================================
name: Documentation
on:
pull_request:
paths:
- 'docs/**'
- 'tutorials/**'
- 'src/**'
- 'Project.toml'
- 'Manifest.toml'
jobs:
docs-build:
runs-on: ubuntu-latest
timeout-minutes: 90
steps:
- name: Cancel Previous Runs
uses: styfle/cancel-workflow-action@0.4.0
with:
access_token: ${{ github.token }}
- uses: actions/checkout@v2.2.0
- name: Install System Dependencies
run: |
sudo apt-get update
sudo apt-get -qq install libxt6 libxrender1 libxext6 libgl1-mesa-glx libqt5widgets5 xvfb
- uses: julia-actions/setup-julia@latest
with:
version: 1.5.4
# https://discourse.julialang.org/t/recommendation-cache-julia-artifacts-in-ci-services/35484
- name: Cache artifacts
uses: actions/cache@v1
env:
cache-name: cache-artifacts
with:
path: ~/.julia/artifacts
key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
restore-keys: |
${{ runner.os }}-test-${{ env.cache-name }}-
${{ runner.os }}-test-
${{ runner.os }}-
- name: Install Julia dependencies
env:
JULIA_PROJECT: "docs/"
run: |
julia --project -e 'using Pkg; Pkg.instantiate()'
julia --project=docs/ -e 'using Pkg; Pkg.instantiate()'
julia --project=docs/ -e 'using Pkg; Pkg.precompile()'
- name: Build and deploy
# Run with X virtual frame buffer as GR (default backend for Plots.jl) needs
# an X session to run without warnings
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
XDG_RUNTIME_DIR: "/home/runner"
JULIA_PROJECT: "docs/"
CLIMATEMACHINE_DOCS_GENERATE_TUTORIALS: "false"
ClIMATEMACHINE_SETTINGS_DISABLE_GPU: "true"
CLIMATEMACHINE_SETTINGS_DISABLE_CUSTOM_LOGGER: "true"
CLIMATEMACHINE_SETTINGS_FIX_RNG_SEED: "true"
run: xvfb-run -- julia --project=docs/ --color=yes docs/make.jl
- name: Help! Documenter Failed
run: |
cat .github/workflows/doc_build_common_error_messages.md
if: failure()
================================================
FILE: .github/workflows/JuliaFormatter.yml
================================================
name: JuliaFormatter
on:
push:
branches:
- master
- trying
- staging
tags: '*'
pull_request:
jobs:
format:
runs-on: ubuntu-latest
timeout-minutes: 30
steps:
- name: Cancel Previous Runs
uses: styfle/cancel-workflow-action@0.4.0
with:
access_token: ${{ github.token }}
- uses: actions/checkout@v2.2.0
- uses: dorny/paths-filter@v2.9.1
id: filter
with:
filters: |
julia_file_change:
- added|modified: '**.jl'
- uses: julia-actions/setup-julia@latest
if: steps.filter.outputs.julia_file_change == 'true'
with:
version: 1.5.4
- name: Apply JuliaFormatter
if: steps.filter.outputs.julia_file_change == 'true'
run: |
julia --project=.dev .dev/climaformat.jl .
- name: Check formatting diff
if: steps.filter.outputs.julia_file_change == 'true'
run: |
git diff --color=always --exit-code
================================================
FILE: .github/workflows/Linux-UnitTests.yml
================================================
name: Unit Tests
on:
pull_request:
paths:
- 'src/**'
- 'test/**'
- 'Project.toml'
- 'Manifest.toml'
jobs:
test:
runs-on: ubuntu-latest
timeout-minutes: 60
strategy:
fail-fast: true
matrix:
test-modules: ["Atmos,Common,InputOutput,Utilities",
"Driver",
"Diagnostics",
"Arrays,Numerics/ODESolvers,Numerics/SystemSolvers",
"Ocean",
"Land",]
env:
CLIMATEMACHINE_SETTINGS_FIX_RNG_SEED: "true"
steps:
- name: Cancel Previous Runs
uses: styfle/cancel-workflow-action@0.4.0
with:
access_token: ${{ github.token }}
- name: Checkout
uses: actions/checkout@v2.2.0
- name: Set up Julia
uses: julia-actions/setup-julia@latest
with:
version: 1.5.4
# https://discourse.julialang.org/t/recommendation-cache-julia-artifacts-in-ci-services/35484
- name: Cache artifacts
uses: actions/cache@v1
env:
cache-name: cache-artifacts
with:
path: ~/.julia/artifacts
key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
restore-keys: |
${{ runner.os }}-test-${{ env.cache-name }}-
${{ runner.os }}-test-
${{ runner.os }}-
- name: Install Project Packages
run: |
julia --project=@. -e 'using Pkg; Pkg.instantiate()'
julia --project=@. -e 'using Pkg; Pkg.precompile()'
- name: Run Unit Tests
env:
TEST_MODULES: ${{ matrix.test-modules }}
run: |
julia --project=@. -e 'using Pkg; Pkg.test(test_args=map(String, split(ENV["TEST_MODULES"], ",")))'
================================================
FILE: .github/workflows/OS-UnitTests.yml
================================================
name: OS Unit Tests
on:
push:
branches:
- staging
- trying
jobs:
test-os:
timeout-minutes: 210
strategy:
fail-fast: true
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
runs-on: ${{ matrix.os }}
# Workaround for OSX MPICH issue:
# https://github.com/pmodels/mpich/issues/4710
env:
MPICH_INTERFACE_HOSTNAME: "localhost"
CLIMATEMACHINE_TEST_RUNMPI_LOCALHOST: "true"
CLIMATEMACHINE_SETTINGS_FIX_RNG_SEED: "true"
steps:
- name: Cancel Previous Runs
uses: styfle/cancel-workflow-action@0.4.0
with:
access_token: ${{ github.token }}
- name: Checkout
uses: actions/checkout@v2.2.0
# Setup a filter and only run if src/ test/ folder content changes
# or project depedencies
- uses: dorny/paths-filter@v2
id: filter
with:
filters: |
run_test:
- 'src/**'
- 'test/**'
- 'Project.toml'
- 'Manifest.toml'
- name: Set up Julia
uses: julia-actions/setup-julia@latest
if: steps.filter.outputs.run_test == 'true'
with:
version: 1.5.4
# https://discourse.julialang.org/t/recommendation-cache-julia-artifacts-in-ci-services/35484
- name: Cache artifacts
uses: actions/cache@v1
if: steps.filter.outputs.run_test == 'true'
env:
cache-name: cache-artifacts
with:
path: ~/.julia/artifacts
key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
restore-keys: |
${{ runner.os }}-test-${{ env.cache-name }}-
${{ runner.os }}-test-
${{ runner.os }}-
- name: Install Project Packages
if: steps.filter.outputs.run_test == 'true'
run: |
julia --project=@. -e 'using Pkg; Pkg.instantiate()'
- name: Build System Image
if: steps.filter.outputs.run_test == 'true'
continue-on-error: true
run: |
julia --project .dev/systemimage/climate_machine_image.jl ClimateMachine.so true
- name: Run Unit Tests
if: steps.filter.outputs.run_test == 'true'
run: |
julia --project -J ClimateMachine.so -e 'using Pkg; Pkg.test()'
================================================
FILE: .github/workflows/PR-Comment.yml
================================================
name: Trigger action on PR comment
on:
issue_comment:
types: [created]
jobs:
trigger-doc-build:
if: ${{ github.event.issue.pull_request &&
( github.event.comment.author_association == 'OWNER' ||
github.event.comment.author_association == 'MEMBER' ||
github.event.comment.author_association == 'COLLABORATOR' ) &&
contains(github.event.comment.body, '@climabot build docs') }}
runs-on: ubuntu-latest
steps:
- uses: octokit/request-action@v2.0.26
id: get_pr # need sha of commit
with:
route: GET /repos/{repository}/pulls/{pull_number}
repository: ${{ github.repository }}
pull_number: ${{ github.event.issue.number }}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Trigger Buildkite Pipeline
id: buildkite
uses: CliMA/buildkite-pipeline-action@master
with:
access_token: ${{ secrets.BUILDKITE }}
pipeline: 'clima/climatemachine-docs'
branch: ${{ fromJson(steps.get_pr.outputs.data).head.ref }}
commit: ${{ fromJson(steps.get_pr.outputs.data).head.sha }}
message: ":github: Triggered by comment on PR #${{ github.event.issue.number }}"
env: '{"PULL_REQUEST": ${{ github.event.issue.number }} }'
async: true
- name: Create comment
uses: peter-evans/create-or-update-comment@v1
with:
issue-number: ${{ github.event.issue.number }}
body: |
Docs build created: ${{ steps.buildkite.outputs.web_url }}
Preview link: https://clima.github.io/ClimateMachine.jl/previews/PR${{ github.event.issue.number}}
================================================
FILE: .github/workflows/doc_build_common_error_messages.md
================================================
# Documenter common warning/error messages:
## General notes
- Changing order of API/HowToGuides does not fix unresolved path issues
## no doc found for reference
```
┌ Warning: no doc found for reference '[`BatchedGeneralizedMinimalResidual`](@ref)' in src/HowToGuides/Numerics/SystemSolvers/IterativeSolvers.md.
└ @ Documenter.CrossReferences ~/.julia/packages/Documenter/PLD7m/src/CrossReferences.jl:160
```
- Missing entry in ```@docs ``` in API
## Reference could not be found
```
┌ Warning: reference for 'ClimateMachine.ODESolvers.solve!' could not be found in src\APIs\Driver\index.md.
└ @ Documenter.CrossReferences C:\Users\kawcz\.julia\packages\Documenter\PLD7m\src\CrossReferences.jl:104
```
- Missing doc string?
## invalid local link: unresolved path
```
┌ Warning: invalid local link: unresolved path in APIs/Atmos/AtmosModel.md
│ link.text =
│ 1-element Array{Any,1}:
│ Markdown.Code("", "FlatOrientation")
│ link.url = "@ref"
```
- Missing entry in ```@docs ``` for FlatOrientation in API OR
- The "code" in the reference must be to actual code and not arbitrary text
## unable to get the binding
```
┌ Warning: unable to get the binding for 'ClimateMachine.Atmos.AtmosModel.NoOrientation' in `@docs` block in src/APIs/Atmos/AtmosModel.md:9-14 from expression ':(ClimateMachine.Atmos.AtmosModel.NoOrientation)' in module ClimateMachine
│ ```@docs
│ ClimateMachine.Atmos.AtmosModel.NoOrientation
...
│ ```
...
```
- `ClimateMachine.Atmos.AtmosModel.NoOrientation` should be `ClimateMachine.Atmos.NoOrientation`
## Other useful tips
- The syntax is white space sensitive: Do not leave any extra new line between the end of the doc string (denoted by triple double-quotes `"""`) and the code of the defined method / type / module name that you are describing.
- In the doc string, indent the method / type / module signature and do not indent the descriptive text.
- Any method name and the corresponding signature in the doc string have to match 1:1 (be careful of missing/extra exclamation points `!`)
================================================
FILE: .gitignore
================================================
# Temporary
*.DS_Store
*.swp
*.jl.cov
*.jl.*.cov
*.jl.mem
*.DS_Store
*~
TAGS
# Docs
docs/build/
docs/site/
docs/src/tutorials/
docs/src/generated/
docs/transient_dir/generated/
!docs/src/assets/*.png
!docs/src/assets/*.svg
# Deps
src/**/Manifest.toml
# Data
*.vtk
*.dat
*.vtu
*.pvtu
*.nc
*.jld2
# Figs
*.png
*.jpg
*.jpeg
*.svg
# Movies
*.gif
*.mp4
# Julia System Images
*.so
================================================
FILE: LICENSE.md
================================================
Copyright 2019 Climate Modeling Alliance
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
================================================
FILE: Manifest.toml
================================================
# This file is machine-generated - editing it directly is not advised
[[AbstractFFTs]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0"
uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
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[[Adapt]]
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git-tree-sha1 = "ffcfa2d345aaee0ef3d8346a073d5dd03c983ebe"
uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
version = "3.2.0"
[[ArgParse]]
deps = ["Logging", "TextWrap"]
git-tree-sha1 = "e928ca0a49f7b0564044b39108c70c160f03e05a"
uuid = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
version = "1.1.2"
[[ArgTools]]
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uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
version = "1.1.1"
[[ArnoldiMethod]]
deps = ["LinearAlgebra", "Random", "StaticArrays"]
git-tree-sha1 = "f87e559f87a45bece9c9ed97458d3afe98b1ebb9"
uuid = "ec485272-7323-5ecc-a04f-4719b315124d"
version = "0.1.0"
[[ArrayInterface]]
deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"]
git-tree-sha1 = "ce17bad65d0842b34a15fffc8879a9f68f08a67f"
uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
version = "3.1.6"
[[ArrayLayouts]]
deps = ["FillArrays", "LinearAlgebra", "SparseArrays"]
git-tree-sha1 = "9aa9647b58147a81f7359eacc7d6249ac3a3e3d4"
uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
version = "0.6.4"
[[ArtifactWrappers]]
deps = ["DocStringExtensions", "Downloads", "Pkg"]
git-tree-sha1 = "e9b52e63e3ea81a504412807c9426566e26c232d"
uuid = "a14bc488-3040-4b00-9dc1-f6467924858a"
version = "0.1.1"
[[Artifacts]]
deps = ["Pkg"]
git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
version = "1.3.0"
[[BFloat16s]]
deps = ["LinearAlgebra", "Test"]
git-tree-sha1 = "4af69e205efc343068dc8722b8dfec1ade89254a"
uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b"
version = "0.1.0"
[[Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
[[BenchmarkTools]]
deps = ["JSON", "Logging", "Printf", "Statistics", "UUIDs"]
git-tree-sha1 = "9e62e66db34540a0c919d72172cc2f642ac71260"
uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
version = "0.5.0"
[[CEnum]]
git-tree-sha1 = "215a9aa4a1f23fbd05b92769fdd62559488d70e9"
uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
version = "0.4.1"
[[CFTime]]
deps = ["Dates", "Printf"]
git-tree-sha1 = "bca6cb6ee746e6485ca4535f6cc29cf3579a0f20"
uuid = "179af706-886a-5703-950a-314cd64e0468"
version = "0.1.1"
[[CLIMAParameters]]
deps = ["Test"]
git-tree-sha1 = "0801216ee1670a1e5280cdb0e5fda60cc4b992ca"
uuid = "6eacf6c3-8458-43b9-ae03-caf5306d3d53"
version = "0.2.0"
[[CUDA]]
deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "DataStructures", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "Logging", "MacroTools", "NNlib", "Pkg", "Printf", "Random", "Reexport", "Requires", "SparseArrays", "Statistics", "TimerOutputs"]
git-tree-sha1 = "6ccc73b2d8b671f7a65c92b5f08f81422ebb7547"
uuid = "052768ef-5323-5732-b1bb-66c8b64840ba"
version = "2.4.1"
[[Cassette]]
git-tree-sha1 = "742fbff99a2798f02bd37d25087efb5615b5a207"
uuid = "7057c7e9-c182-5462-911a-8362d720325c"
version = "0.3.5"
[[ChainRulesCore]]
deps = ["Compat", "LinearAlgebra", "SparseArrays"]
git-tree-sha1 = "644c24cd6344348f1c645efab24b707088be526a"
uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
version = "0.9.34"
[[CloudMicrophysics]]
deps = ["CLIMAParameters", "DocStringExtensions", "SpecialFunctions", "Thermodynamics"]
git-tree-sha1 = "52c85d99a842a1d9ebf6f36e8dd34d55e903b0b5"
uuid = "6a9e3e04-43cd-43ba-94b9-e8782df3c71b"
version = "0.3.1"
[[CodecZlib]]
deps = ["TranscodingStreams", "Zlib_jll"]
git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da"
uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
version = "0.7.0"
[[Combinatorics]]
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[[CommonSolve]]
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[[CommonSubexpressions]]
deps = ["MacroTools", "Test"]
git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7"
uuid = "bbf7d656-a473-5ed7-a52c-81e309532950"
version = "0.3.0"
[[Compat]]
deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
git-tree-sha1 = "919c7f3151e79ff196add81d7f4e45d91bbf420b"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
version = "3.25.0"
[[CompilerSupportLibraries_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "8e695f735fca77e9708e795eda62afdb869cbb70"
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
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[[ConstructionBase]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "48920211c95a6da1914a06c44ec94be70e84ffff"
uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
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[[Coverage]]
deps = ["CoverageTools", "HTTP", "JSON", "LibGit2", "MbedTLS"]
git-tree-sha1 = "a485b62b1ce53368e3a1a3a8dc0c39a61b9d3d9c"
uuid = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
version = "1.2.0"
[[CoverageTools]]
deps = ["LibGit2"]
git-tree-sha1 = "08b72d2f2154e33dc2aeb1bfcd4a83cb283abd4f"
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[[Crayons]]
git-tree-sha1 = "3f71217b538d7aaee0b69ab47d9b7724ca8afa0d"
uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
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[[CubedSphere]]
deps = ["Elliptic", "Printf", "Rotations", "TaylorSeries", "Test"]
git-tree-sha1 = "f66fabd1ee5df59a7ba47c7873a6332c19e0c03f"
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[[DataAPI]]
git-tree-sha1 = "dfb3b7e89e395be1e25c2ad6d7690dc29cc53b1d"
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[[DataStructures]]
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[[DataValueInterfaces]]
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[[Dates]]
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[[Dierckx]]
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[[Dierckx_jll]]
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[[DiffEqBase]]
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git-tree-sha1 = "c2ff625248a0967adff1dc1f79c6a41e2531f081"
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[[DiffRules]]
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[[Distributed]]
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[[Distributions]]
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[[GPUArrays]]
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[[GPUCompiler]]
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[[GaussQuadrature]]
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================================================
FILE: Project.toml
================================================
name = "ClimateMachine"
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authors = ["Climate Modeling Alliance"]
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================================================
FILE: README.md
================================================
# ClimateMachine.jl
***NOTE THAT THIS REPO IS NOT CURRENTLY BEING MAINTAINED. PLEASE SEE THE FOLLOWING REPOSITORIES:***
- [CliMA/ClimaCore.jl](http://github.com/CliMA/ClimaCore.jl)
- [CliMA/ClimaAtmos.jl](http://github.com/CliMA/ClimaAtmos.jl)
- [CliMA/Thermodynamics.jl](http://github.com/CliMA/Thermodynamics.jl)
- [CliMA/CloudMicrophysics.jl](http://github.com/CliMA/CloudMicrophysics.jl)
- [CliMA/SurfaceFluxes.jl](http://github.com/CliMA/SurfaceFluxes.jl)
- [CliMA/ClimaLSM.jl](http://github.com/CliMA/ClimaLSM.jl)
- [CliMA/Oceananigans.jl](http://github.com/CliMA/Oceananigans.jl)
- [CliMA/ClimaCoupler.jl](http://github.com/CliMA/ClimaCoupler.jl)
The Climate Machine is a new Earth system model that leverages recent advances in the computational and data sciences to learn directly from a wealth of Earth observations from space and the ground. The Climate Machine will harness more data than ever before, providing a new level of accuracy to predictions of droughts, heat waves, and rainfall extremes.
| **Documentation** | [![dev][docs-latest-img]][docs-latest-url] |
|----------------------|--------------------------------------------------|
| **Docs Build** | [![docs build][docs-bld-img]][docs-bld-url] |
| **Unit tests** | [![unit tests][unit-tests-img]][unit-tests-url] |
| **Code Coverage** | [![codecov][codecov-img]][codecov-url] |
| **Bors** | [![Bors enabled][bors-img]][bors-url] |
| **DOI** | [![Zenodo][zenodo-img]][zenodo-url] |
[docs-bld-img]: https://github.com/CliMA/ClimateMachine.jl/workflows/Documentation/badge.svg
[docs-bld-url]: https://github.com/CliMA/ClimateMachine.jl/actions?query=workflow%3ADocumentation
[docs-latest-img]: https://img.shields.io/badge/docs-latest-blue.svg
[docs-latest-url]: https://CliMA.github.io/ClimateMachine.jl/latest/
[unit-tests-img]: https://github.com/CliMA/ClimateMachine.jl/workflows/OS%20Unit%20Tests/badge.svg
[unit-tests-url]: https://github.com/CliMA/ClimateMachine.jl/actions?query=workflow%3A%22OS+Unit+Tests%22
[codecov-img]: https://codecov.io/gh/CliMA/ClimateMachine.jl/branch/master/graph/badge.svg
[codecov-url]: https://codecov.io/gh/CliMA/ClimateMachine.jl
[bors-img]: https://bors.tech/images/badge_small.svg
[bors-url]: https://app.bors.tech/repositories/11521
[zenodo-img]: https://zenodo.org/badge/162166244.svg
[zenodo-url]: https://zenodo.org/badge/latestdoi/162166244
For installation instructions and explanations on how to use the Climate Machine, please look at the [Documentation](https://clima.github.io/ClimateMachine.jl/latest/GettingStarted/Installation/).
================================================
FILE: bors.toml
================================================
status = [
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"test-os (windows-latest)",
"test-os (macos-latest)",
"buildkite/climatemachine-ci",
"buildkite/climatemachine-docs",
"format"
]
delete_merged_branches = true
timeout_sec = 12600
block_labels = [ "do-not-merge-yet" ]
cut_body_after = "<!--"
required_approvals = 1
================================================
FILE: docs/Manifest.toml
================================================
# This file is machine-generated - editing it directly is not advised
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FILE: docs/bibliography.bib
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d
gitextract_rqfc0vw8/
├── .buildkite/
│ ├── docs-pipeline.yml
│ └── pipeline.yml
├── .codecov.yml
├── .dev/
│ ├── .gitignore
│ ├── Project.toml
│ ├── clima_formatter_default_image.jl
│ ├── clima_formatter_image.jl
│ ├── clima_formatter_options.jl
│ ├── climaformat.jl
│ ├── hooks/
│ │ ├── pre-commit
│ │ └── pre-commit.sysimage
│ ├── precompile.jl
│ └── systemimage/
│ └── climate_machine_image.jl
├── .github/
│ ├── issue_template.md
│ ├── pull_request_template.md
│ └── workflows/
│ ├── CompatHelper.yml
│ ├── Coverage.yaml
│ ├── DocCleanup.yml
│ ├── Documenter.yaml
│ ├── JuliaFormatter.yml
│ ├── Linux-UnitTests.yml
│ ├── OS-UnitTests.yml
│ ├── PR-Comment.yml
│ └── doc_build_common_error_messages.md
├── .gitignore
├── LICENSE.md
├── Manifest.toml
├── Project.toml
├── README.md
├── bors.toml
├── docs/
│ ├── Manifest.toml
│ ├── Project.toml
│ ├── bibliography.bib
│ ├── clean_build_folder.jl
│ ├── list_of_apis.jl
│ ├── list_of_dev_docs.jl
│ ├── list_of_getting_started_docs.jl
│ ├── list_of_how_to_guides.jl
│ ├── list_of_theory_docs.jl
│ ├── list_of_tutorials.jl
│ ├── make.jl
│ ├── pages_helper.jl
│ ├── plothelpers.jl
│ └── src/
│ ├── APIs/
│ │ ├── Arrays/
│ │ │ └── Arrays.md
│ │ ├── Atmos/
│ │ │ └── AtmosModel.md
│ │ ├── BalanceLaws/
│ │ │ ├── BalanceLaws.md
│ │ │ └── Problems.md
│ │ ├── Common/
│ │ │ ├── CartesianDomains.md
│ │ │ ├── CartesianFields.md
│ │ │ ├── Orientations.md
│ │ │ ├── Spectra.md
│ │ │ ├── TurbulenceClosures.md
│ │ │ └── TurbulenceConvection.md
│ │ ├── Diagnostics/
│ │ │ ├── Diagnostics.md
│ │ │ ├── DiagnosticsMachine.md
│ │ │ ├── StateCheck.md
│ │ │ └── StdDiagnostics.md
│ │ ├── Driver/
│ │ │ ├── Checkpoint.md
│ │ │ └── index.md
│ │ ├── InputOutput/
│ │ │ └── index.md
│ │ ├── Land/
│ │ │ ├── LandModel.md
│ │ │ ├── RadiativeEnergyFlux.md
│ │ │ ├── Runoff.md
│ │ │ ├── SoilHeatParameterizations.md
│ │ │ ├── SoilWaterParameterizations.md
│ │ │ └── SurfaceFlow.md
│ │ ├── Numerics/
│ │ │ ├── DGMethods/
│ │ │ │ ├── Courant.md
│ │ │ │ ├── DGMethods.md
│ │ │ │ ├── FVReconstructions.md
│ │ │ │ └── NumericalFluxes.md
│ │ │ ├── Meshes/
│ │ │ │ └── Mesh.md
│ │ │ ├── ODESolvers/
│ │ │ │ └── ODESolvers.md
│ │ │ └── SystemSolvers/
│ │ │ └── SystemSolvers.md
│ │ ├── Ocean/
│ │ │ └── Ocean.md
│ │ ├── Utilities/
│ │ │ ├── SingleStackUtils.md
│ │ │ ├── TicToc.md
│ │ │ └── VariableTemplates.md
│ │ └── index.md
│ ├── Contributing.md
│ ├── DevDocs/
│ │ ├── AcceptableUnicode.md
│ │ ├── CodeStyle.md
│ │ ├── DiagnosticVariableList.md
│ │ ├── ModelOutput.md
│ │ ├── ModelVariableList.md
│ │ └── SystemImage.md
│ ├── GettingStarted/
│ │ ├── Atmos.md
│ │ ├── Installation.md
│ │ ├── RunningClimateMachine.md
│ │ └── Terminology.md
│ ├── HowToGuides/
│ │ ├── Atmos/
│ │ │ ├── AtmosReferenceState.md
│ │ │ ├── MoistureAndPrecip.md
│ │ │ ├── MoistureModelChoices.md
│ │ │ └── PrecipitationModelChoices.md
│ │ ├── BalanceLaws/
│ │ │ └── how_to_make_a_balance_law.md
│ │ ├── Diagnostics/
│ │ │ └── UsingDiagnostics.md
│ │ ├── Land/
│ │ │ └── index.md
│ │ ├── Numerics/
│ │ │ ├── Meshes/
│ │ │ │ └── index.md
│ │ │ ├── ODESolvers/
│ │ │ │ └── Timestepping.md
│ │ │ └── SystemSolvers/
│ │ │ └── IterativeSolvers.md
│ │ └── Ocean/
│ │ └── index.md
│ ├── References.md
│ ├── Theory/
│ │ ├── Atmos/
│ │ │ ├── AtmosModel.md
│ │ │ ├── EDMFEquations.md
│ │ │ ├── EDMF_plots.md
│ │ │ ├── Microphysics_0M.md
│ │ │ ├── Microphysics_1M.md
│ │ │ └── Model/
│ │ │ └── tracers.md
│ │ └── Common/
│ │ └── Turbulence.md
│ └── index.md
├── experiments/
│ ├── AtmosGCM/
│ │ ├── GCMDriver/
│ │ │ ├── GCMDriver.jl
│ │ │ ├── baroclinicwave_problem.jl
│ │ │ ├── gcm_base_states.jl
│ │ │ ├── gcm_bcs.jl
│ │ │ ├── gcm_moisture_profiles.jl
│ │ │ ├── gcm_perturbations.jl
│ │ │ ├── gcm_sources.jl
│ │ │ └── heldsuarez_problem.jl
│ │ ├── heldsuarez.jl
│ │ ├── moist_baroclinic_wave_bulksfcflux.jl
│ │ └── nonhydrostatic_gravity_wave.jl
│ ├── AtmosLES/
│ │ ├── Artifacts.toml
│ │ ├── bomex_les.jl
│ │ ├── bomex_model.jl
│ │ ├── bomex_single_stack.jl
│ │ ├── cfsite_hadgem2-a_07_amip.jl
│ │ ├── convective_bl_les.jl
│ │ ├── convective_bl_model.jl
│ │ ├── dycoms.jl
│ │ ├── ekman_layer_model.jl
│ │ ├── rising_bubble_bryan.jl
│ │ ├── rising_bubble_theta_formulation.jl
│ │ ├── schar_scalar_advection.jl
│ │ ├── squall_line.jl
│ │ ├── stable_bl_les.jl
│ │ ├── stable_bl_model.jl
│ │ ├── surfacebubble.jl
│ │ └── taylor_green.jl
│ ├── OceanBoxGCM/
│ │ ├── homogeneous_box.jl
│ │ ├── ocean_gyre.jl
│ │ └── simple_box.jl
│ ├── OceanSplitExplicit/
│ │ └── simple_box.jl
│ └── TestCase/
│ ├── baroclinic_wave.jl
│ ├── baroclinic_wave_fvm.jl
│ ├── isothermal_zonal_flow.jl
│ ├── risingbubble.jl
│ ├── risingbubble_fvm.jl
│ ├── solid_body_rotation.jl
│ ├── solid_body_rotation_fvm.jl
│ └── solid_body_rotation_mountain.jl
├── src/
│ ├── Arrays/
│ │ ├── CMBuffers.jl
│ │ └── MPIStateArrays.jl
│ ├── Atmos/
│ │ ├── Model/
│ │ │ ├── AtmosModel.jl
│ │ │ ├── atmos_tendencies.jl
│ │ │ ├── bc_energy.jl
│ │ │ ├── bc_initstate.jl
│ │ │ ├── bc_moisture.jl
│ │ │ ├── bc_momentum.jl
│ │ │ ├── bc_precipitation.jl
│ │ │ ├── bc_tracer.jl
│ │ │ ├── boundaryconditions.jl
│ │ │ ├── courant.jl
│ │ │ ├── declare_prognostic_vars.jl
│ │ │ ├── energy.jl
│ │ │ ├── filters.jl
│ │ │ ├── get_prognostic_vars.jl
│ │ │ ├── linear.jl
│ │ │ ├── linear_atmos_tendencies.jl
│ │ │ ├── linear_tendencies.jl
│ │ │ ├── lsforcing.jl
│ │ │ ├── moisture.jl
│ │ │ ├── multiphysics_types.jl
│ │ │ ├── precipitation.jl
│ │ │ ├── problem.jl
│ │ │ ├── prog_prim_conversion.jl
│ │ │ ├── projections.jl
│ │ │ ├── radiation.jl
│ │ │ ├── reconstructions.jl
│ │ │ ├── ref_state.jl
│ │ │ ├── tendencies_energy.jl
│ │ │ ├── tendencies_mass.jl
│ │ │ ├── tendencies_moisture.jl
│ │ │ ├── tendencies_momentum.jl
│ │ │ ├── tendencies_precipitation.jl
│ │ │ ├── tendencies_tracers.jl
│ │ │ ├── thermo_states.jl
│ │ │ ├── thermo_states_anelastic.jl
│ │ │ └── tracers.jl
│ │ ├── Parameterizations/
│ │ │ ├── GravityWaves/
│ │ │ │ └── README.md
│ │ │ ├── README.md
│ │ │ └── Radiation/
│ │ │ └── README.md
│ │ └── TemperatureProfiles/
│ │ └── TemperatureProfiles.jl
│ ├── BalanceLaws/
│ │ ├── BalanceLaws.jl
│ │ ├── Problems.jl
│ │ ├── boundaryconditions.jl
│ │ ├── interface.jl
│ │ ├── kernels.jl
│ │ ├── prog_prim_conversion.jl
│ │ ├── show_tendencies.jl
│ │ ├── state_types.jl
│ │ ├── sum_tendencies.jl
│ │ ├── tendency_types.jl
│ │ └── vars_wrappers.jl
│ ├── ClimateMachine.jl
│ ├── Common/
│ │ ├── CartesianDomains/
│ │ │ ├── CartesianDomains.jl
│ │ │ └── rectangular_domain.jl
│ │ ├── CartesianFields/
│ │ │ ├── CartesianFields.jl
│ │ │ ├── rectangular_element.jl
│ │ │ └── rectangular_spectral_element_fields.jl
│ │ ├── Orientations/
│ │ │ └── Orientations.jl
│ │ ├── Spectra/
│ │ │ ├── Spectra.jl
│ │ │ ├── power_spectrum_gcm.jl
│ │ │ ├── power_spectrum_les.jl
│ │ │ └── spherical_helper.jl
│ │ ├── SurfaceFluxes/
│ │ │ └── README.md
│ │ ├── TurbulenceClosures/
│ │ │ └── TurbulenceClosures.jl
│ │ └── TurbulenceConvection/
│ │ ├── TurbulenceConvection.jl
│ │ ├── boundary_conditions.jl
│ │ └── source.jl
│ ├── Diagnostics/
│ │ ├── Debug/
│ │ │ └── StateCheck.jl
│ │ ├── Diagnostics.jl
│ │ ├── DiagnosticsMachine/
│ │ │ ├── DiagnosticsMachine.jl
│ │ │ ├── atmos_diagnostic_funs.jl
│ │ │ ├── group_gen.jl
│ │ │ ├── groups.jl
│ │ │ ├── horizontal_average.jl
│ │ │ ├── onetime.jl
│ │ │ ├── pointwise.jl
│ │ │ └── variables.jl
│ │ ├── StdDiagnostics/
│ │ │ ├── StdDiagnostics.jl
│ │ │ ├── atmos_gcm_default.jl
│ │ │ ├── atmos_gcm_diagnostic_vars.jl
│ │ │ ├── atmos_les_default.jl
│ │ │ └── atmos_les_diagnostic_vars.jl
│ │ ├── atmos_common.jl
│ │ ├── atmos_gcm_default.jl
│ │ ├── atmos_gcm_spectra.jl
│ │ ├── atmos_les_core.jl
│ │ ├── atmos_les_default.jl
│ │ ├── atmos_les_default_perturbations.jl
│ │ ├── atmos_les_spectra.jl
│ │ ├── atmos_mass_energy_loss.jl
│ │ ├── atmos_refstate_perturbations.jl
│ │ ├── atmos_turbulence_stats.jl
│ │ ├── diagnostic_fields.jl
│ │ ├── dump_aux.jl
│ │ ├── dump_init.jl
│ │ ├── dump_state.jl
│ │ ├── dump_tendencies.jl
│ │ ├── groups.jl
│ │ ├── helpers.jl
│ │ ├── thermo.jl
│ │ ├── variables.jl
│ │ └── vorticity_balancelaw.jl
│ ├── Driver/
│ │ ├── Callbacks/
│ │ │ └── Callbacks.jl
│ │ ├── Checkpoint/
│ │ │ └── Checkpoint.jl
│ │ ├── ConfigTypes/
│ │ │ └── ConfigTypes.jl
│ │ ├── Driver.jl
│ │ ├── SolverTypes/
│ │ │ ├── ExplicitSolverType.jl
│ │ │ ├── HEVISolverType.jl
│ │ │ ├── IMEXSolverType.jl
│ │ │ ├── ImplicitSolverType.jl
│ │ │ ├── MISSolverType.jl
│ │ │ ├── MultirateSolverType.jl
│ │ │ ├── SolverTypes.jl
│ │ │ └── SplitExplicitSolverType.jl
│ │ ├── diagnostics_configs.jl
│ │ ├── driver_configs.jl
│ │ ├── solver_config_wrappers.jl
│ │ └── solver_configs.jl
│ ├── InputOutput/
│ │ ├── VTK/
│ │ │ ├── VTK.jl
│ │ │ ├── fieldwriter.jl
│ │ │ ├── writemesh.jl
│ │ │ ├── writepvtu.jl
│ │ │ └── writevtk.jl
│ │ └── Writers/
│ │ ├── Writers.jl
│ │ └── netcdf_writer.jl
│ ├── LICENSE
│ ├── Land/
│ │ └── Model/
│ │ ├── LandModel.jl
│ │ ├── RadiativeEnergyFlux.jl
│ │ ├── Runoff.jl
│ │ ├── SoilHeatParameterizations.jl
│ │ ├── SoilWaterParameterizations.jl
│ │ ├── SurfaceFlow.jl
│ │ ├── land_bc.jl
│ │ ├── land_tendencies.jl
│ │ ├── prog_types.jl
│ │ ├── prognostic_vars.jl
│ │ ├── soil_bc.jl
│ │ ├── soil_heat.jl
│ │ ├── soil_model.jl
│ │ ├── soil_water.jl
│ │ └── source.jl
│ ├── Numerics/
│ │ ├── DGMethods/
│ │ │ ├── Courant.jl
│ │ │ ├── DGFVModel.jl
│ │ │ ├── DGFVModel_kernels.jl
│ │ │ ├── DGMethods.jl
│ │ │ ├── DGModel.jl
│ │ │ ├── DGModel_kernels.jl
│ │ │ ├── ESDGModel.jl
│ │ │ ├── ESDGModel_kernels.jl
│ │ │ ├── FVReconstructions.jl
│ │ │ ├── NumericalFluxes.jl
│ │ │ ├── SpaceDiscretization.jl
│ │ │ ├── create_states.jl
│ │ │ ├── custom_filter.jl
│ │ │ └── remainder.jl
│ │ ├── Mesh/
│ │ │ ├── BrickMesh.jl
│ │ │ ├── DSS.jl
│ │ │ ├── Elements.jl
│ │ │ ├── Filters.jl
│ │ │ ├── GeometricFactors.jl
│ │ │ ├── Geometry.jl
│ │ │ ├── Grids.jl
│ │ │ ├── Interpolation.jl
│ │ │ ├── Mesh.jl
│ │ │ ├── Metrics.jl
│ │ │ └── Topologies.jl
│ │ ├── ODESolvers/
│ │ │ ├── AdditiveRungeKuttaMethod.jl
│ │ │ ├── BackwardEulerSolvers.jl
│ │ │ ├── DifferentialEquations.jl
│ │ │ ├── GenericCallbacks.jl
│ │ │ ├── LowStorageRungeKutta3NMethod.jl
│ │ │ ├── LowStorageRungeKuttaMethod.jl
│ │ │ ├── MultirateInfinitesimalGARKDecoupledImplicit.jl
│ │ │ ├── MultirateInfinitesimalGARKExplicit.jl
│ │ │ ├── MultirateInfinitesimalStepMethod.jl
│ │ │ ├── MultirateRungeKuttaMethod.jl
│ │ │ ├── ODESolvers.jl
│ │ │ ├── SplitExplicitMethod.jl
│ │ │ └── StrongStabilityPreservingRungeKuttaMethod.jl
│ │ └── SystemSolvers/
│ │ ├── SystemSolvers.jl
│ │ ├── batched_generalized_minimal_residual_solver.jl
│ │ ├── columnwise_lu_solver.jl
│ │ ├── conjugate_gradient_solver.jl
│ │ ├── generalized_conjugate_residual_solver.jl
│ │ ├── generalized_minimal_residual_solver.jl
│ │ ├── jacobian_free_newton_krylov_solver.jl
│ │ └── preconditioners.jl
│ ├── Ocean/
│ │ ├── HydrostaticBoussinesq/
│ │ │ ├── Courant.jl
│ │ │ ├── HydrostaticBoussinesq.jl
│ │ │ ├── LinearHBModel.jl
│ │ │ ├── bc_temperature.jl
│ │ │ ├── bc_velocity.jl
│ │ │ └── hydrostatic_boussinesq_model.jl
│ │ ├── JLD2Writer.jl
│ │ ├── Ocean.jl
│ │ ├── OceanBC.jl
│ │ ├── OceanProblems/
│ │ │ ├── OceanProblems.jl
│ │ │ ├── homogeneous_box.jl
│ │ │ ├── initial_value_problem.jl
│ │ │ ├── ocean_gyre.jl
│ │ │ ├── shallow_water_initial_states.jl
│ │ │ └── simple_box_problem.jl
│ │ ├── README.md
│ │ ├── ShallowWater/
│ │ │ ├── ShallowWaterModel.jl
│ │ │ └── bc_velocity.jl
│ │ ├── SplitExplicit/
│ │ │ ├── Communication.jl
│ │ │ ├── HydrostaticBoussinesqCoupling.jl
│ │ │ ├── ShallowWaterCoupling.jl
│ │ │ ├── SplitExplicitModel.jl
│ │ │ └── VerticalIntegralModel.jl
│ │ ├── SplitExplicit01/
│ │ │ ├── BarotropicModel.jl
│ │ │ ├── Communication.jl
│ │ │ ├── Continuity3dModel.jl
│ │ │ ├── IVDCModel.jl
│ │ │ ├── OceanBoundaryConditions.jl
│ │ │ ├── OceanModel.jl
│ │ │ ├── SplitExplicitLSRK2nMethod.jl
│ │ │ ├── SplitExplicitLSRK3nMethod.jl
│ │ │ ├── SplitExplicitModel.jl
│ │ │ └── VerticalIntegralModel.jl
│ │ └── SuperModels.jl
│ └── Utilities/
│ ├── SingleStackUtils/
│ │ ├── SingleStackUtils.jl
│ │ └── single_stack_diagnostics.jl
│ ├── TicToc/
│ │ └── TicToc.jl
│ └── VariableTemplates/
│ ├── VariableTemplates.jl
│ ├── flattened_tup_chain.jl
│ └── var_names.jl
├── test/
│ ├── Arrays/
│ │ ├── basics.jl
│ │ ├── broadcasting.jl
│ │ ├── mpi_comm.jl
│ │ ├── reductions.jl
│ │ ├── runtests.jl
│ │ └── varsindex.jl
│ ├── Atmos/
│ │ ├── EDMF/
│ │ │ ├── Artifacts.toml
│ │ │ ├── bomex_edmf.jl
│ │ │ ├── closures/
│ │ │ │ ├── entr_detr.jl
│ │ │ │ ├── mixing_length.jl
│ │ │ │ ├── pressure.jl
│ │ │ │ ├── surface_functions.jl
│ │ │ │ └── turbulence_functions.jl
│ │ │ ├── compute_mse.jl
│ │ │ ├── edmf_kernels.jl
│ │ │ ├── edmf_model.jl
│ │ │ ├── ekman_layer.jl
│ │ │ ├── helper_funcs/
│ │ │ │ ├── diagnose_environment.jl
│ │ │ │ ├── diagnostics_configuration.jl
│ │ │ │ ├── lamb_smooth_minimum.jl
│ │ │ │ ├── nondimensional_exchange_functions.jl
│ │ │ │ ├── save_subdomain_temperature.jl
│ │ │ │ ├── subdomain_statistics.jl
│ │ │ │ ├── subdomain_thermo_states.jl
│ │ │ │ └── utility_funcs.jl
│ │ │ ├── report_mse_bomex.jl
│ │ │ ├── report_mse_sbl_anelastic.jl
│ │ │ ├── report_mse_sbl_coupled_edmf_an1d.jl
│ │ │ ├── report_mse_sbl_edmf.jl
│ │ │ ├── report_mse_sbl_ss_implicit.jl
│ │ │ ├── stable_bl_anelastic1d.jl
│ │ │ ├── stable_bl_coupled_edmf_an1d.jl
│ │ │ ├── stable_bl_edmf.jl
│ │ │ ├── stable_bl_edmf_fvm.jl
│ │ │ ├── stable_bl_single_stack_implicit.jl
│ │ │ └── variable_map.jl
│ │ ├── Model/
│ │ │ ├── Artifacts.toml
│ │ │ ├── discrete_hydrostatic_balance.jl
│ │ │ ├── get_atmos_ref_states.jl
│ │ │ ├── ref_state.jl
│ │ │ └── runtests.jl
│ │ ├── Parameterizations/
│ │ │ └── Microphysics/
│ │ │ ├── KM_ice.jl
│ │ │ ├── KM_saturation_adjustment.jl
│ │ │ ├── KM_warm_rain.jl
│ │ │ └── KinematicModel.jl
│ │ ├── prog_prim_conversion/
│ │ │ └── runtests.jl
│ │ └── runtests.jl
│ ├── BalanceLaws/
│ │ └── runtests.jl
│ ├── Common/
│ │ ├── CartesianDomains/
│ │ │ └── runtests.jl
│ │ ├── CartesianFields/
│ │ │ └── runtests.jl
│ │ ├── Spectra/
│ │ │ ├── gcm_standalone_visual_test.jl
│ │ │ ├── runtests.jl
│ │ │ └── spherical_helper_test.jl
│ │ └── runtests.jl
│ ├── Diagnostics/
│ │ ├── Debug/
│ │ │ ├── test_statecheck.jl
│ │ │ └── test_statecheck_refvals.jl
│ │ ├── diagnostic_fields_test.jl
│ │ ├── dm_tests.jl
│ │ ├── runtests.jl
│ │ ├── sin_init.jl
│ │ └── sin_test.jl
│ ├── Driver/
│ │ ├── cr_unit_tests.jl
│ │ ├── gcm_driver_test.jl
│ │ ├── les_driver_test.jl
│ │ ├── mms3.jl
│ │ └── runtests.jl
│ ├── InputOutput/
│ │ ├── VTK/
│ │ │ └── runtests.jl
│ │ ├── Writers/
│ │ │ └── runtests.jl
│ │ └── runtests.jl
│ ├── Land/
│ │ ├── Model/
│ │ │ ├── Artifacts.toml
│ │ │ ├── freeze_thaw_alone.jl
│ │ │ ├── haverkamp_test.jl
│ │ │ ├── heat_analytic_unit_test.jl
│ │ │ ├── prescribed_twice.jl
│ │ │ ├── runtests.jl
│ │ │ ├── soil_heterogeneity.jl
│ │ │ ├── test_bc.jl
│ │ │ ├── test_bc_3d.jl
│ │ │ ├── test_heat_parameterizations.jl
│ │ │ ├── test_overland_flow_analytic.jl
│ │ │ ├── test_overland_flow_vcatchment.jl
│ │ │ ├── test_physical_bc.jl
│ │ │ ├── test_radiative_energy_flux_functions.jl
│ │ │ └── test_water_parameterizations.jl
│ │ └── runtests.jl
│ ├── Numerics/
│ │ ├── DGMethods/
│ │ │ ├── Euler/
│ │ │ │ ├── acousticwave_1d_imex.jl
│ │ │ │ ├── acousticwave_mrigark.jl
│ │ │ │ ├── acousticwave_variable_degree.jl
│ │ │ │ ├── fvm_balance.jl
│ │ │ │ ├── fvm_isentropicvortex.jl
│ │ │ │ ├── isentropicvortex.jl
│ │ │ │ ├── isentropicvortex_imex.jl
│ │ │ │ ├── isentropicvortex_lmars.jl
│ │ │ │ ├── isentropicvortex_mrigark.jl
│ │ │ │ ├── isentropicvortex_mrigark_implicit.jl
│ │ │ │ ├── isentropicvortex_multirate.jl
│ │ │ │ └── isentropicvortex_setup.jl
│ │ │ ├── advection_diffusion/
│ │ │ │ ├── advection_diffusion_model.jl
│ │ │ │ ├── advection_diffusion_model_1dimex_bgmres.jl
│ │ │ │ ├── advection_diffusion_model_1dimex_bjfnks.jl
│ │ │ │ ├── advection_sphere.jl
│ │ │ │ ├── diffusion_hyperdiffusion_sphere.jl
│ │ │ │ ├── direction_splitting_advection_diffusion.jl
│ │ │ │ ├── fvm_advection.jl
│ │ │ │ ├── fvm_advection_diffusion.jl
│ │ │ │ ├── fvm_advection_diffusion_model_1dimex_bjfnks.jl
│ │ │ │ ├── fvm_advection_diffusion_periodic.jl
│ │ │ │ ├── fvm_advection_sphere.jl
│ │ │ │ ├── fvm_swirl.jl
│ │ │ │ ├── hyperdiffusion_bc.jl
│ │ │ │ ├── hyperdiffusion_model.jl
│ │ │ │ ├── periodic_3D_hyperdiffusion.jl
│ │ │ │ ├── pseudo1D_advection_diffusion.jl
│ │ │ │ ├── pseudo1D_advection_diffusion_1dimex.jl
│ │ │ │ ├── pseudo1D_advection_diffusion_mrigark_implicit.jl
│ │ │ │ ├── pseudo1D_heat_eqn.jl
│ │ │ │ └── variable_degree_advection_diffusion.jl
│ │ │ ├── compressible_Navier_Stokes/
│ │ │ │ ├── density_current_model.jl
│ │ │ │ ├── mms_bc_atmos.jl
│ │ │ │ ├── mms_bc_dgmodel.jl
│ │ │ │ ├── mms_model.jl
│ │ │ │ ├── mms_solution.jl
│ │ │ │ └── mms_solution_generated.jl
│ │ │ ├── compressible_navier_stokes_equations/
│ │ │ │ ├── plotting/
│ │ │ │ │ ├── bigfileofstuff.jl
│ │ │ │ │ ├── plot_output.jl
│ │ │ │ │ └── vizinanigans.jl
│ │ │ │ ├── shared_source/
│ │ │ │ │ ├── FluidBC.jl
│ │ │ │ │ ├── ScalarFields.jl
│ │ │ │ │ ├── VectorFields.jl
│ │ │ │ │ ├── abstractions.jl
│ │ │ │ │ ├── boilerplate.jl
│ │ │ │ │ ├── callbacks.jl
│ │ │ │ │ ├── domains.jl
│ │ │ │ │ └── grids.jl
│ │ │ │ ├── sphere/
│ │ │ │ │ ├── sphere_helper_functions.jl
│ │ │ │ │ ├── test_heat_equation.jl
│ │ │ │ │ ├── test_hydrostatic_balance.jl
│ │ │ │ │ └── test_sphere.jl
│ │ │ │ ├── three_dimensional/
│ │ │ │ │ ├── ThreeDimensionalCompressibleNavierStokesEquations.jl
│ │ │ │ │ ├── bc_momentum.jl
│ │ │ │ │ ├── bc_temperature.jl
│ │ │ │ │ ├── config_sphere.jl
│ │ │ │ │ ├── refvals_bickley_jet.jl
│ │ │ │ │ ├── refvals_buoyancy.jl
│ │ │ │ │ ├── run_bickley_jet.jl
│ │ │ │ │ ├── run_box.jl
│ │ │ │ │ ├── run_taylor_green_vortex.jl
│ │ │ │ │ ├── test_bickley_jet.jl
│ │ │ │ │ └── test_buoyancy.jl
│ │ │ │ └── two_dimensional/
│ │ │ │ ├── TwoDimensionalCompressibleNavierStokesEquations.jl
│ │ │ │ ├── bc_momentum.jl
│ │ │ │ ├── bc_tracer.jl
│ │ │ │ ├── refvals_bickley_jet.jl
│ │ │ │ ├── run_bickley_jet.jl
│ │ │ │ └── test_bickley_jet.jl
│ │ │ ├── conservation/
│ │ │ │ └── sphere.jl
│ │ │ ├── courant.jl
│ │ │ ├── custom_filter.jl
│ │ │ ├── fv_reconstruction_test.jl
│ │ │ ├── grad_test.jl
│ │ │ ├── grad_test_sphere.jl
│ │ │ ├── horizontal_integral_test.jl
│ │ │ ├── integral_test.jl
│ │ │ ├── integral_test_sphere.jl
│ │ │ ├── remainder_model.jl
│ │ │ └── vars_test.jl
│ │ ├── ESDGMethods/
│ │ │ ├── DryAtmos/
│ │ │ │ ├── DryAtmos.jl
│ │ │ │ ├── baroclinic_wave.jl
│ │ │ │ ├── linear.jl
│ │ │ │ ├── run_tests.jl
│ │ │ │ └── run_tests_mpo.jl
│ │ │ └── diagnostics.jl
│ │ ├── Mesh/
│ │ │ ├── BrickMesh.jl
│ │ │ ├── DSS.jl
│ │ │ ├── DSS_mpi.jl
│ │ │ ├── Elements.jl
│ │ │ ├── Geometry.jl
│ │ │ ├── Grids.jl
│ │ │ ├── Metrics.jl
│ │ │ ├── filter.jl
│ │ │ ├── filter_TMAR.jl
│ │ │ ├── grid_integral.jl
│ │ │ ├── interpolation.jl
│ │ │ ├── min_node_distance.jl
│ │ │ ├── mpi_centroid.jl
│ │ │ ├── mpi_connect.jl
│ │ │ ├── mpi_connect_1d.jl
│ │ │ ├── mpi_connect_ell.jl
│ │ │ ├── mpi_connect_sphere.jl
│ │ │ ├── mpi_connect_stacked.jl
│ │ │ ├── mpi_connect_stacked_3d.jl
│ │ │ ├── mpi_connectfull.jl
│ │ │ ├── mpi_getpartition.jl
│ │ │ ├── mpi_partition.jl
│ │ │ ├── mpi_sortcolumns.jl
│ │ │ └── topology.jl
│ │ ├── ODESolvers/
│ │ │ ├── callbacks.jl
│ │ │ ├── ode_tests_basic.jl
│ │ │ ├── ode_tests_common.jl
│ │ │ ├── ode_tests_convergence.jl
│ │ │ └── runtests.jl
│ │ ├── SystemSolvers/
│ │ │ ├── bandedsystem.jl
│ │ │ ├── bgmres.jl
│ │ │ ├── cg.jl
│ │ │ ├── columnwiselu.jl
│ │ │ ├── iterativesolvers.jl
│ │ │ ├── poisson.jl
│ │ │ └── runtests.jl
│ │ └── runtests.jl
│ ├── Ocean/
│ │ ├── HydrostaticBoussinesq/
│ │ │ ├── test_3D_spindown.jl
│ │ │ ├── test_initial_value_problem.jl
│ │ │ ├── test_ocean_gyre_long.jl
│ │ │ ├── test_ocean_gyre_short.jl
│ │ │ ├── test_windstress_long.jl
│ │ │ └── test_windstress_short.jl
│ │ ├── HydrostaticBoussinesqModel/
│ │ │ └── test_hydrostatic_boussinesq_model.jl
│ │ ├── OceanProblems/
│ │ │ └── test_initial_value_problem.jl
│ │ ├── ShallowWater/
│ │ │ ├── GyreDriver.jl
│ │ │ └── test_2D_spindown.jl
│ │ ├── SplitExplicit/
│ │ │ ├── hydrostatic_spindown.jl
│ │ │ ├── simple_box_2dt.jl
│ │ │ ├── simple_box_ivd.jl
│ │ │ ├── simple_box_rk3.jl
│ │ │ ├── simple_dbl_gyre.jl
│ │ │ ├── split_explicit.jl
│ │ │ ├── test_coriolis.jl
│ │ │ ├── test_restart.jl
│ │ │ ├── test_simple_box.jl
│ │ │ ├── test_spindown_long.jl
│ │ │ ├── test_spindown_short.jl
│ │ │ └── test_vertical_integral_model.jl
│ │ ├── refvals/
│ │ │ ├── 2D_hydrostatic_spindown_refvals.jl
│ │ │ ├── 3D_hydrostatic_spindown_refvals.jl
│ │ │ ├── hydrostatic_spindown_refvals.jl
│ │ │ ├── simple_box_2dt_refvals.jl
│ │ │ ├── simple_box_ivd_refvals.jl
│ │ │ ├── simple_box_rk3_refvals.jl
│ │ │ ├── simple_dbl_gyre_refvals.jl
│ │ │ ├── test_ocean_gyre_refvals.jl
│ │ │ ├── test_vertical_integral_model_refvals.jl
│ │ │ └── test_windstress_refvals.jl
│ │ └── runtests.jl
│ ├── Utilities/
│ │ ├── SingleStackUtils/
│ │ │ ├── runtests.jl
│ │ │ └── ssu_tests.jl
│ │ ├── TicToc/
│ │ │ └── runtests.jl
│ │ ├── VariableTemplates/
│ │ │ ├── complex_models.jl
│ │ │ ├── runtests.jl
│ │ │ ├── runtests_gpu.jl
│ │ │ ├── test_base_functionality.jl
│ │ │ ├── test_complex_models.jl
│ │ │ ├── test_complex_models_gpu.jl
│ │ │ └── varsindex.jl
│ │ └── runtests.jl
│ ├── runtests.jl
│ ├── runtests_gpu.jl
│ └── testhelpers.jl
└── tutorials/
├── Atmos/
│ ├── agnesi_hs_lin.jl
│ ├── agnesi_nh_lin.jl
│ ├── burgers_single_stack.jl
│ ├── burgers_single_stack_bjfnk.jl
│ ├── burgers_single_stack_fvm.jl
│ ├── densitycurrent.jl
│ ├── dry_rayleigh_benard.jl
│ ├── heldsuarez.jl
│ └── risingbubble.jl
├── BalanceLaws/
│ └── tendency_specification_layer.jl
├── Diagnostics/
│ └── Debug/
│ └── StateCheck.jl
├── Land/
│ ├── Heat/
│ │ └── heat_equation.jl
│ └── Soil/
│ ├── Artifacts.toml
│ ├── Coupled/
│ │ └── equilibrium_test.jl
│ ├── Heat/
│ │ └── bonan_heat_tutorial.jl
│ ├── PhaseChange/
│ │ ├── freezing_front.jl
│ │ └── phase_change_analytic_test.jl
│ ├── Water/
│ │ ├── equilibrium_test.jl
│ │ └── hydraulic_functions.jl
│ └── interpolation_helper.jl
├── Numerics/
│ ├── DGMethods/
│ │ ├── Box1D.jl
│ │ └── showcase_filters.jl
│ ├── SystemSolvers/
│ │ ├── bgmres.jl
│ │ └── cg.jl
│ └── TimeStepping/
│ ├── explicit_lsrk.jl
│ ├── imex_ark.jl
│ ├── mis.jl
│ ├── multirate_rk.jl
│ ├── ts_intro.jl
│ ├── tutorial_acousticwave_config.jl
│ └── tutorial_risingbubble_config.jl
├── Ocean/
│ ├── geostrophic_adjustment.jl
│ ├── internal_wave.jl
│ └── shear_instability.jl
├── TutorialList.jl
└── literate_markdown.jl
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"path": "docs/Project.toml",
"chars": 1779,
"preview": "[deps]\nArgParse = \"c7e460c6-2fb9-53a9-8c5b-16f535851c63\"\nCLIMAParameters = \"6eacf6c3-8458-43b9-ae03-caf5306d3d53\"\nDataFr"
},
{
"path": "docs/bibliography.bib",
"chars": 36257,
"preview": "# The citation keys have been formatted as:\n# Last author name (titlecase), followed by\n# (no characters in-betwee"
},
{
"path": "docs/clean_build_folder.jl",
"chars": 567,
"preview": "#####\n##### make sure there are no temporary files files (e.g., *.vtu) left around from the build in `GENERATED_DIR`\n###"
},
{
"path": "docs/list_of_apis.jl",
"chars": 2521,
"preview": "####\n#### Defines list of Application Programming Interface (APIs)\n####\n\napis = [\n \"Home\" => \"APIs/index.md\",\n \"Dr"
},
{
"path": "docs/list_of_dev_docs.jl",
"chars": 411,
"preview": "####\n#### Defines list of developer documents\n####\n\ndev_docs = Any[\n \"Coding style\" => \"DevDocs/CodeStyle.md\",\n \"A"
},
{
"path": "docs/list_of_getting_started_docs.jl",
"chars": 346,
"preview": "####\n#### Defines list of getting started documents\n####\n\ngetting_started_docs = Any[\n \"Installation\" => \"GettingStar"
},
{
"path": "docs/list_of_how_to_guides.jl",
"chars": 1142,
"preview": "####\n#### Defines list of how-to-guides\n####\n\nhow_to_guides = Any[\n \"Balance Laws\" => Any[\"How to make a balance law\""
},
{
"path": "docs/list_of_theory_docs.jl",
"chars": 526,
"preview": "####\n#### Defines list of theory documents\n####\n\ntheory_docs = Any[\n \"Common\" => Any[\"Turbulence Closures\" => \"Theory"
},
{
"path": "docs/list_of_tutorials.jl",
"chars": 5542,
"preview": "####\n#### Defines list of tutorials given `GENERATED_DIR`\n####\n\ngenerate_tutorials =\n parse(Bool, get(ENV, \"CLIMATEMA"
},
{
"path": "docs/make.jl",
"chars": 2693,
"preview": "# https://github.com/jheinen/GR.jl/issues/278#issuecomment-587090846\nENV[\"GKSwstype\"] = \"nul\"\n# some of the tutorials ca"
},
{
"path": "docs/pages_helper.jl",
"chars": 1177,
"preview": "\"\"\"\n get_second\n\nGets `second` in nested array of `Pair`s\nand filters empty entries.\n\"\"\"\nfunction get_second end\n\nget"
},
{
"path": "docs/plothelpers.jl",
"chars": 6858,
"preview": "using Plots\nusing KernelAbstractions: CPU\nusing ClimateMachine.MPIStateArrays: array_device\nusing ClimateMachine.Balance"
},
{
"path": "docs/src/APIs/Arrays/Arrays.md",
"chars": 322,
"preview": "# Arrays\n\n```@meta\nCurrentModule = ClimateMachine.MPIStateArrays\n```\n## MPI State Arrays\n\nStorage for the state of a dis"
},
{
"path": "docs/src/APIs/Atmos/AtmosModel.md",
"chars": 2622,
"preview": "# [AtmosModel](@id AtmosModel-docs)\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\n## AtmosProblem\n\n```@docs\nClimateMachi"
},
{
"path": "docs/src/APIs/BalanceLaws/BalanceLaws.md",
"chars": 1508,
"preview": "# Balance Laws\n\n```@meta\nCurrentModule = ClimateMachine.BalanceLaws\n```\n\n## The balance law\n\n```@docs\nBalanceLaw\n```\n\n##"
},
{
"path": "docs/src/APIs/BalanceLaws/Problems.md",
"chars": 200,
"preview": "# Problems\n\n```@meta\nCurrentModule = ClimateMachine.Problems\n```\n\n## The problem\n\n```@docs\nAbstractProblem\n```\n\n## Initi"
},
{
"path": "docs/src/APIs/Common/CartesianDomains.md",
"chars": 114,
"preview": "# Cartesian Domains\n\n```@meta\nCurrentModule = ClimateMachine.CartesianDomains\n```\n\n```@docs\nRectangularDomain\n```\n"
},
{
"path": "docs/src/APIs/Common/CartesianFields.md",
"chars": 143,
"preview": "# Cartesian Fields\n\n```@meta\nCurrentModule = ClimateMachine.CartesianFields\n```\n\n```@docs\nSpectralElementField\nRectangul"
},
{
"path": "docs/src/APIs/Common/Orientations.md",
"chars": 209,
"preview": "# Orientations\n\n```@meta\nCurrentModule = ClimateMachine.Orientations\n```\n\n```@docs\nOrientations\n```\n\n## Types\n\n```@docs\n"
},
{
"path": "docs/src/APIs/Common/Spectra.md",
"chars": 143,
"preview": "# Spectra\n\n```@meta\nCurrentModule = ClimateMachine.Spectra\n```\n\n## Methods\n\n```@docs\npower_spectrum_1d\npower_spectrum_2d"
},
{
"path": "docs/src/APIs/Common/TurbulenceClosures.md",
"chars": 588,
"preview": "# TurbulenceClosures\n\n```@meta\nCurrentModule = ClimateMachine.TurbulenceClosures\n```\n\n```@docs\nTurbulenceClosures\n```\n\n#"
},
{
"path": "docs/src/APIs/Common/TurbulenceConvection.md",
"chars": 233,
"preview": "# Turbulence Convection\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\n```@docs\nTurbulenceConvection\n```\n\n## Models\n\n```@"
},
{
"path": "docs/src/APIs/Diagnostics/Diagnostics.md",
"chars": 877,
"preview": "# [Diagnostics](@id Diagnostics-docs)\n\n```@meta\nCurrentModule = ClimateMachine.Diagnostics\n```\n\n```@docs\nDiagnostics\n```"
},
{
"path": "docs/src/APIs/Diagnostics/DiagnosticsMachine.md",
"chars": 1563,
"preview": "# [DiagnosticsMachine](@id DiagnosticsMachine)\n\n```@meta\nCurrentModule = ClimateMachine.DiagnosticsMachine\n```\n\n```@docs"
},
{
"path": "docs/src/APIs/Diagnostics/StateCheck.md",
"chars": 233,
"preview": "# State Check\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\n```@docs\nClimateMachine.StateCheck\n```\n\n## Methods\n\n```@docs"
},
{
"path": "docs/src/APIs/Diagnostics/StdDiagnostics.md",
"chars": 2160,
"preview": "# [StdDiagnostics](@id StdDiagnostics)\n\n```@meta\nCurrentModule = ClimateMachine.StdDiagnostics\n```\n\n```@docs\nStdDiagnost"
},
{
"path": "docs/src/APIs/Driver/Checkpoint.md",
"chars": 142,
"preview": "# Checkpoint\n\n```@meta\nCurrentModule = ClimateMachine.Checkpoint\n```\n\n## Methods\n\n```@docs\nrm_checkpoint\nread_checkpoint"
},
{
"path": "docs/src/APIs/Driver/index.md",
"chars": 516,
"preview": "# Driver\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\n## Solver types and functions\n\n```@docs\nHEVISplitting\nMISSolverTy"
},
{
"path": "docs/src/APIs/InputOutput/index.md",
"chars": 210,
"preview": "# Input/Output\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\n## VTK\n\n```@docs\nVTK.writevtk\nVTK.writepvtu\nVTK.VTKFieldWri"
},
{
"path": "docs/src/APIs/Land/LandModel.md",
"chars": 905,
"preview": "# Land Model\n\n```@meta\nCurrentModule = ClimateMachine\n```\n## Land Model\n\n```@docs\nClimateMachine.Land.LandModel\n```\n\n## "
},
{
"path": "docs/src/APIs/Land/RadiativeEnergyFlux.md",
"chars": 271,
"preview": "# RadiativeEnergyFlux\n\n```@meta\nCurrentModule = ClimateMachine.Land.RadiativeEnergyFlux\n```\n\n## RadiativeEnergyFlux type"
},
{
"path": "docs/src/APIs/Land/Runoff.md",
"chars": 227,
"preview": "# Runoff\n\n```@meta\nCurrentModule = ClimateMachine.Land.Runoff\n```\n\n## Runoff types and functions\n```@docs\nAbstractPrecip"
},
{
"path": "docs/src/APIs/Land/SoilHeatParameterizations.md",
"chars": 371,
"preview": "# Soil Heat Parameterizations\n\n```@meta\nCurrentModule = ClimateMachine.Land.SoilHeatParameterizations\n```\n\n## Heat funct"
},
{
"path": "docs/src/APIs/Land/SoilWaterParameterizations.md",
"chars": 577,
"preview": "# Soil Water Parameterizations\n\n```@meta\nCurrentModule = ClimateMachine.Land.SoilWaterParameterizations\n```\n\n## Water fu"
},
{
"path": "docs/src/APIs/Land/SurfaceFlow.md",
"chars": 269,
"preview": "# SurfaceFlow\n\n```@meta\nCurrentModule = ClimateMachine.Land.SurfaceFlow\n```\n\n## SurfaceFlow types and functions\n```@docs"
},
{
"path": "docs/src/APIs/Numerics/DGMethods/Courant.md",
"chars": 195,
"preview": "# Discontinuous Galerkin Methods\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\n## Functions\n\n```@docs\nCourant\nCourant.ad"
},
{
"path": "docs/src/APIs/Numerics/DGMethods/DGMethods.md",
"chars": 478,
"preview": "# Discontinuous Galerkin Methods\n\n```@meta\nCurrentModule = ClimateMachine.DGMethods\n```\n\n```@docs\nSpaceDiscretization\nDG"
},
{
"path": "docs/src/APIs/Numerics/DGMethods/FVReconstructions.md",
"chars": 218,
"preview": "# Numerical Fluxes\n\n```@meta\nCurrentModule = ClimateMachine.DGMethods.FVReconstructions\n```\n\n## Types\n\n```@docs\n Abst"
},
{
"path": "docs/src/APIs/Numerics/DGMethods/NumericalFluxes.md",
"chars": 374,
"preview": "# Numerical Fluxes\n\n```@meta\nCurrentModule = ClimateMachine.DGMethods.NumericalFluxes\n```\n\n## Types\n\n```@docs\nNumericalF"
},
{
"path": "docs/src/APIs/Numerics/Meshes/Mesh.md",
"chars": 2835,
"preview": "# Meshing Stuff\n\n```@meta\nCurrentModule = ClimateMachine.Mesh\n```\n\n## Topologies\n\nTopologies encode the connectivity of "
},
{
"path": "docs/src/APIs/Numerics/ODESolvers/ODESolvers.md",
"chars": 2338,
"preview": "# [ODESolvers](@id ODESolvers-docs)\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\n```@docs\nODESolvers\n```\n\n## Low Storag"
},
{
"path": "docs/src/APIs/Numerics/SystemSolvers/SystemSolvers.md",
"chars": 952,
"preview": "# System Solvers\n\n```@meta\nCurrentModule = ClimateMachine.SystemSolvers\n```\n\n## Non-linear solvers\n\n```@docs\nLSOnly\nJaco"
},
{
"path": "docs/src/APIs/Ocean/Ocean.md",
"chars": 970,
"preview": "# Ocean Base Module\n\n```@meta\nCurrentModule = ClimateMachine.Ocean\n```\n\n# Hydrostatic Boussinesq\n\n```@meta\nCurrentModule"
},
{
"path": "docs/src/APIs/Utilities/SingleStackUtils.md",
"chars": 328,
"preview": "# Single Stack Utils\n\n```@meta\nCurrentModule = ClimateMachine.SingleStackUtils\n```\n\n## Functions\n\n```@docs\nget_vars_from"
},
{
"path": "docs/src/APIs/Utilities/TicToc.md",
"chars": 156,
"preview": "# Tic Toc\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\n```@docs\nClimateMachine.TicToc\n```\n\n## Methods\n\n```@docs\nTicToc."
},
{
"path": "docs/src/APIs/Utilities/VariableTemplates.md",
"chars": 269,
"preview": "# Variable Templates\n\n```@meta\nCurrentModule = ClimateMachine.VariableTemplates\n```\n\n## Types\n\n```@docs\nGrad\nVars\n```\n\n#"
},
{
"path": "docs/src/APIs/index.md",
"chars": 237,
"preview": "# Application Programming Interface (APIs)\n\nHere, references are provided for ClimateMachine's programming interface. Th"
},
{
"path": "docs/src/Contributing.md",
"chars": 10536,
"preview": "# Contributing\n\nThank you for considering contributing to the `ClimateMachine`! We encourage\nPull Requests (PRs). Please"
},
{
"path": "docs/src/DevDocs/AcceptableUnicode.md",
"chars": 998,
"preview": "# Acceptable Unicode characters\n\nUsing Unicode seems to be irresistible. However, we must ensure avoiding\nproblematic Un"
},
{
"path": "docs/src/DevDocs/CodeStyle.md",
"chars": 5098,
"preview": "# Coding conventions\n\nFor the most part, we follow the\n[YASGuide](https://github.com/jrevels/YASGuide). Some key conside"
},
{
"path": "docs/src/DevDocs/DiagnosticVariableList.md",
"chars": 16009,
"preview": "# [Diagnostic Variable List](@id Diagnostics-vars)\n\nThis is a list of all the diagnostic variables that the `ClimateMach"
},
{
"path": "docs/src/DevDocs/ModelOutput.md",
"chars": 1741,
"preview": "# [ClimateMachine Output](@id Model-output)\n\nThese are the output data types currently supported by the `ClimateMachine`"
},
{
"path": "docs/src/DevDocs/ModelVariableList.md",
"chars": 4106,
"preview": "# ClimateMachine Variable List\n\nThis document is currently for collaborators within the project with\naccess to the Overl"
},
{
"path": "docs/src/DevDocs/SystemImage.md",
"chars": 1692,
"preview": "# System Image\n\nTo speed up the start time of `ClimateMachine` a custom system image can be\nbuilt with the\n[`PackageComp"
},
{
"path": "docs/src/GettingStarted/Atmos.md",
"chars": 2150,
"preview": "# Atmosphere model configurations\n\nThe struct `AtmosModel` defines a specific subtype of a balance law\n(i.e. conservatio"
},
{
"path": "docs/src/GettingStarted/Installation.md",
"chars": 2474,
"preview": "# Installing ClimateMachine\n\n## Install Julia\n\nThe Climate Machine (CLIMA) uses the Julia programming language and has b"
},
{
"path": "docs/src/GettingStarted/RunningClimateMachine.md",
"chars": 11796,
"preview": "# Running the `ClimateMachine`\n\nThe `ClimateMachine` is composed of three models for the Earth system,\na dynamical core,"
},
{
"path": "docs/src/GettingStarted/Terminology.md",
"chars": 5275,
"preview": "# Terminology\n\nThe `ClimateMachine` documentation uses terminology from several disciplines. Below are some definitions "
},
{
"path": "docs/src/HowToGuides/Atmos/AtmosReferenceState.md",
"chars": 1310,
"preview": "# Atmospheric temperature profiles\n\nHere, we plot the atmospheric reference state profiles for a few different polynomia"
},
{
"path": "docs/src/HowToGuides/Atmos/MoistureAndPrecip.md",
"chars": 11135,
"preview": "## Representing moisture and precipitation\n\nThis tutorial shows how to setup an Atmos experiment with moisture\n(i.e. wat"
},
{
"path": "docs/src/HowToGuides/Atmos/MoistureModelChoices.md",
"chars": 4938,
"preview": "# Moisture model choices in Atmos.jl\n\nThe moisture model in `Atmos.jl` describes the behavior\n of suspended water in th"
},
{
"path": "docs/src/HowToGuides/Atmos/PrecipitationModelChoices.md",
"chars": 1762,
"preview": "# Precipitation model choices in Atmos.jl\n\nThe precipitation model in `Atmos.jl` describes the behavior\n of precipitati"
},
{
"path": "docs/src/HowToGuides/BalanceLaws/how_to_make_a_balance_law.md",
"chars": 6552,
"preview": "# How to make a Balance law\n\n```@meta\nCurrentModule = ClimateMachine.BalanceLaws\n```\n\nDefining the set of solved PDEs in"
},
{
"path": "docs/src/HowToGuides/Diagnostics/UsingDiagnostics.md",
"chars": 3433,
"preview": "# [Using Diagnostics](@id How-to-diagnostics)\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\nAn experiment can configure "
},
{
"path": "docs/src/HowToGuides/Land/index.md",
"chars": 8,
"preview": "# Land\n\n"
},
{
"path": "docs/src/HowToGuides/Numerics/Meshes/index.md",
"chars": 9,
"preview": "# Meshes\n"
},
{
"path": "docs/src/HowToGuides/Numerics/ODESolvers/Timestepping.md",
"chars": 11467,
"preview": "# Contribution Guide for Abstract Time-stepping Algorithms\n\n```@meta\nCurrentModule = ClimateMachine.ODESolvers\n```\n\nThis"
},
{
"path": "docs/src/HowToGuides/Numerics/SystemSolvers/IterativeSolvers.md",
"chars": 8441,
"preview": "# Contribution Guide for Abstract Iterative Solvers\n\n```@meta\nCurrentModule = ClimateMachine.SystemSolvers\n```\n\nAn abstr"
},
{
"path": "docs/src/HowToGuides/Ocean/index.md",
"chars": 9,
"preview": "# Ocean\n\n"
},
{
"path": "docs/src/References.md",
"chars": 36,
"preview": "# References\n\n```@bibliography\n```\n\n"
},
{
"path": "docs/src/Theory/Atmos/AtmosModel.md",
"chars": 4186,
"preview": "# Atmos Model\n\nThis page provides a summary of a specific type of balance law within the\n`ClimateMachine` source code, t"
},
{
"path": "docs/src/Theory/Atmos/EDMFEquations.md",
"chars": 40486,
"preview": "```math\n\\newcommand{\\paramT}[1]{ \\text{#1}}\n\\newcommand{\\hyperparamT}[1]{\\text{#1}}\n\\newcommand{\\simparamT}[1]{ \\"
},
{
"path": "docs/src/Theory/Atmos/EDMF_plots.md",
"chars": 1425,
"preview": "# Atmospheric EDMF parameterization profiles\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\nSeveral EDMF related profiles"
},
{
"path": "docs/src/Theory/Atmos/Microphysics_0M.md",
"chars": 2089,
"preview": "# Microphysics_0M\n\nWe are using the `Microphysics_0M.jl` module\n from the [CloudMicrophysics.jl](https://github.com/Cli"
},
{
"path": "docs/src/Theory/Atmos/Microphysics_1M.md",
"chars": 7854,
"preview": "# Microphysics\n\nWe are using the `Microphysics_1M.jl` module\n from the [CloudMicrophysics.jl](https://github.com/CliMA/"
},
{
"path": "docs/src/Theory/Atmos/Model/tracers.md",
"chars": 3384,
"preview": "# [Tracers](@id Tracers-docs)\n\n!!! note\n\n Usage: Enable tracers using a keyword argument in the AtmosModel\n specif"
},
{
"path": "docs/src/Theory/Common/Turbulence.md",
"chars": 7006,
"preview": "## [Turbulence Closures](@id Turbulence-Closures-docs)\nModule `TurbulenceClosures.jl` currently supports \npointwise mode"
},
{
"path": "docs/src/index.md",
"chars": 2376,
"preview": "# ClimateMachine\n\n```@meta\nCurrentModule = ClimateMachine\n```\n\nThe `ClimateMachine` is a software package that models th"
},
{
"path": "experiments/AtmosGCM/GCMDriver/GCMDriver.jl",
"chars": 13104,
"preview": "#!/usr/bin/env julia --project\n\n# This file is the entry point for a generalized GCM driver that is used\n# to run a vari"
},
{
"path": "experiments/AtmosGCM/GCMDriver/baroclinicwave_problem.jl",
"chars": 1422,
"preview": "# This file establishes the default initial conditions, boundary conditions and sources\n# for the baroclinicwave_problem"
},
{
"path": "experiments/AtmosGCM/GCMDriver/gcm_base_states.jl",
"chars": 3634,
"preview": "# GCM Initial Base State\n# This file contains helpers and lists currely avaiable options\n\nabstract type AbstractBaseStat"
},
{
"path": "experiments/AtmosGCM/GCMDriver/gcm_bcs.jl",
"chars": 3089,
"preview": "# GCM Boundary Conditions\n# This file contains helpers and lists currely avaiable options\n\n# Helper for parsing `--surfa"
},
{
"path": "experiments/AtmosGCM/GCMDriver/gcm_moisture_profiles.jl",
"chars": 2301,
"preview": "# GCM Initial Moisture Profiles\n# This file contains helpers and lists currely avaiable options\n\nabstract type AbstractM"
},
{
"path": "experiments/AtmosGCM/GCMDriver/gcm_perturbations.jl",
"chars": 2588,
"preview": "# GCM Initial Perturbation\n# This file contains helpers and lists currely avaiable options\n\nusing Distributions\nusing Ra"
},
{
"path": "experiments/AtmosGCM/GCMDriver/gcm_sources.jl",
"chars": 2203,
"preview": "# GCM-specific Sources\n# This file contains helpers and lists currently available options\n\n# Current options for GCM-spe"
},
{
"path": "experiments/AtmosGCM/GCMDriver/heldsuarez_problem.jl",
"chars": 1745,
"preview": "# This file establishes the default initial conditions, boundary conditions and sources\n# for the heldsuarez_problem exp"
},
{
"path": "experiments/AtmosGCM/heldsuarez.jl",
"chars": 9087,
"preview": "#!/usr/bin/env julia --project\nusing ClimateMachine\nusing ArgParse\nusing UnPack\n\ns = ArgParseSettings()\n@add_arg_table! "
},
{
"path": "experiments/AtmosGCM/moist_baroclinic_wave_bulksfcflux.jl",
"chars": 12753,
"preview": "#!/usr/bin/env julia --project\n\nusing ArgParse\nusing LinearAlgebra\nusing StaticArrays\nusing Test\n\nusing ClimateMachine\nu"
},
{
"path": "experiments/AtmosGCM/nonhydrostatic_gravity_wave.jl",
"chars": 6568,
"preview": "#!/usr/bin/env julia --project\nusing ClimateMachine\nClimateMachine.init(parse_clargs = true)\n\nusing ClimateMachine.Atmos"
},
{
"path": "experiments/AtmosLES/Artifacts.toml",
"chars": 143,
"preview": "[lsforcing]\ngit-tree-sha1 = \"6ac99861047fc1b2c16caa81506bde25e197dc0a\"\n\n[soundings]\ngit-tree-sha1 = \"54fd0eef5f47c4f3266"
},
{
"path": "experiments/AtmosLES/bomex_les.jl",
"chars": 4450,
"preview": "using Random\ninclude(\"bomex_model.jl\")\n\nfunction add_perturbations!(state, localgeo)\n FT = eltype(state)\n z = loca"
},
{
"path": "experiments/AtmosLES/bomex_model.jl",
"chars": 14938,
"preview": "#!/usr/bin/env julia --project\n#=\n# This experiment file establishes the initial conditions, boundary conditions,\n# sour"
},
{
"path": "experiments/AtmosLES/bomex_single_stack.jl",
"chars": 3407,
"preview": "include(\"bomex_model.jl\")\n\nfunction main()\n # add a command line argument to specify the kind of surface flux\n # T"
},
{
"path": "experiments/AtmosLES/cfsite_hadgem2-a_07_amip.jl",
"chars": 17784,
"preview": "# General Julia modules\nusing ArgParse\nusing Dierckx\nusing Distributions\nusing DocStringExtensions\nusing LinearAlgebra\nu"
},
{
"path": "experiments/AtmosLES/convective_bl_les.jl",
"chars": 2079,
"preview": "include(\"convective_bl_model.jl\")\nfunction main()\n\n # TODO: this will move to the future namelist functionality\n c"
},
{
"path": "experiments/AtmosLES/convective_bl_model.jl",
"chars": 9593,
"preview": "#!/usr/bin/env julia --project\n# This experiment file establishes the initial conditions, boundary conditions,\n# source "
},
{
"path": "experiments/AtmosLES/dycoms.jl",
"chars": 14914,
"preview": "#!/usr/bin/env julia --project\nusing ClimateMachine\n\nusing ClimateMachine.Atmos\nusing ClimateMachine.Orientations\nusing "
},
{
"path": "experiments/AtmosLES/ekman_layer_model.jl",
"chars": 8702,
"preview": "#!/usr/bin/env julia --project\n#=\n# This experiment file establishes the initial conditions, boundary conditions,\n# sour"
},
{
"path": "experiments/AtmosLES/rising_bubble_bryan.jl",
"chars": 7585,
"preview": "using ClimateMachine\n\nusing ClimateMachine.Atmos\nusing ClimateMachine.Orientations\nusing ClimateMachine.ConfigTypes\nusin"
},
{
"path": "experiments/AtmosLES/rising_bubble_theta_formulation.jl",
"chars": 15261,
"preview": "# # Rising Thermal Bubble\n#\n# In this example, we demonstrate the usage of the `ClimateMachine`\n# [AtmosModel](@ref Atmo"
},
{
"path": "experiments/AtmosLES/schar_scalar_advection.jl",
"chars": 7906,
"preview": "using ClimateMachine\nClimateMachine.init(parse_clargs = true)\n\nusing ClimateMachine.Atmos\nusing ClimateMachine.Orientati"
},
{
"path": "experiments/AtmosLES/squall_line.jl",
"chars": 16183,
"preview": "using ArgParse\nusing Random\nusing StaticArrays\nusing NCDatasets\nusing Test\nusing DocStringExtensions\nusing LinearAlgebra"
},
{
"path": "experiments/AtmosLES/stable_bl_les.jl",
"chars": 2646,
"preview": "using Random\n\ninclude(\"stable_bl_model.jl\")\n\nfunction add_perturbations!(state, localgeo)\n FT = eltype(state)\n z ="
},
{
"path": "experiments/AtmosLES/stable_bl_model.jl",
"chars": 10435,
"preview": "#!/usr/bin/env julia --project\n#=\n# This experiment file establishes the initial conditions, boundary conditions,\n# sour"
},
{
"path": "experiments/AtmosLES/surfacebubble.jl",
"chars": 5533,
"preview": "#!/usr/bin/env julia --project\nusing ClimateMachine\nClimateMachine.init(parse_clargs = true)\n\nusing ClimateMachine.Atmos"
},
{
"path": "experiments/AtmosLES/taylor_green.jl",
"chars": 6468,
"preview": "#!/usr/bin/env julia --project\n\nusing ClimateMachine\nClimateMachine.init(parse_clargs = true)\n\nusing ClimateMachine.Atmo"
},
{
"path": "experiments/OceanBoxGCM/homogeneous_box.jl",
"chars": 858,
"preview": "#!/usr/bin/env julia --project\n\ninclude(\"simple_box.jl\")\nClimateMachine.init(parse_clargs = true)\n\n# Float type\nconst FT"
},
{
"path": "experiments/OceanBoxGCM/ocean_gyre.jl",
"chars": 853,
"preview": "#!/usr/bin/env julia --project\n\ninclude(\"simple_box.jl\")\nClimateMachine.init(parse_clargs = true)\n\n# Float type\nconst FT"
},
{
"path": "experiments/OceanBoxGCM/simple_box.jl",
"chars": 3145,
"preview": "using Test\nusing ClimateMachine\nusing ClimateMachine.GenericCallbacks\nusing ClimateMachine.ODESolvers\nusing ClimateMachi"
},
{
"path": "experiments/OceanSplitExplicit/simple_box.jl",
"chars": 7503,
"preview": "using Test\nusing MPI\n\nusing ClimateMachine\nusing ClimateMachine.GenericCallbacks\nusing ClimateMachine.ODESolvers\n\nusing "
},
{
"path": "experiments/TestCase/baroclinic_wave.jl",
"chars": 10852,
"preview": "#!/usr/bin/env julia --project\n\nusing ArgParse\nusing LinearAlgebra\nusing StaticArrays\nusing Test\n\nusing ClimateMachine\nu"
},
{
"path": "experiments/TestCase/baroclinic_wave_fvm.jl",
"chars": 10350,
"preview": "#!/usr/bin/env julia --project\n\nusing ArgParse\nusing LinearAlgebra\nusing StaticArrays\nusing Test\n\nusing ClimateMachine\nu"
},
{
"path": "experiments/TestCase/isothermal_zonal_flow.jl",
"chars": 6456,
"preview": "#!/usr/bin/env julia --project\nusing ClimateMachine\nClimateMachine.init(parse_clargs = true)\n\nusing ClimateMachine.Atmos"
},
{
"path": "experiments/TestCase/risingbubble.jl",
"chars": 6318,
"preview": "#!/usr/bin/env julia --project\nusing ArgParse\n\nusing ClimateMachine\nusing ClimateMachine.Atmos\nusing ClimateMachine.Orie"
},
{
"path": "experiments/TestCase/risingbubble_fvm.jl",
"chars": 6762,
"preview": "#!/usr/bin/env julia --project\nusing ArgParse\n\nusing ClimateMachine\nusing ClimateMachine.Atmos\nusing ClimateMachine.Orie"
},
{
"path": "experiments/TestCase/solid_body_rotation.jl",
"chars": 6333,
"preview": "#!/usr/bin/env julia --project\nusing ClimateMachine\nClimateMachine.init(parse_clargs = true)\n\nusing ClimateMachine.Atmos"
},
{
"path": "experiments/TestCase/solid_body_rotation_fvm.jl",
"chars": 6983,
"preview": "#!/usr/bin/env julia --project\nusing ClimateMachine\nClimateMachine.init(parse_clargs = true)\n\nusing ClimateMachine.Atmos"
},
{
"path": "experiments/TestCase/solid_body_rotation_mountain.jl",
"chars": 7069,
"preview": "#!/usr/bin/env julia --project\nusing ClimateMachine\nClimateMachine.init(parse_clargs = true)\n\nusing ClimateMachine.Atmos"
},
{
"path": "src/Arrays/CMBuffers.jl",
"chars": 2935,
"preview": "module CMBuffers\n\nimport CUDA\n\nusing MPI\nusing KernelAbstractions\nusing StaticArrays\n\nexport CMBuffer\nexport SingleCMBuf"
},
{
"path": "src/Arrays/MPIStateArrays.jl",
"chars": 25146,
"preview": "module MPIStateArrays\n\nusing CUDA\nusing DoubleFloats\nusing KernelAbstractions\nusing LazyArrays\nusing LinearAlgebra\nusing"
},
{
"path": "src/Atmos/Model/AtmosModel.jl",
"chars": 44440,
"preview": "module Atmos\n\nexport AtmosModel,\n AtmosPhysics,\n AtmosAcousticLinearModel,\n AtmosAcousticGravityLinearModel,\n "
},
{
"path": "src/Atmos/Model/atmos_tendencies.jl",
"chars": 3391,
"preview": "#####\n##### Tendency specification\n#####\n\n#####\n##### Sources\n#####\n\neq_tends(pv::AbstractPrognosticVariable, m::AtmosMo"
},
{
"path": "src/Atmos/Model/bc_energy.jl",
"chars": 7094,
"preview": "abstract type EnergyBC end\n\nusing ..TurbulenceClosures\nusing SurfaceFluxes: get_energy_flux, surface_conditions, DGSchem"
},
{
"path": "src/Atmos/Model/bc_initstate.jl",
"chars": 1092,
"preview": "using ..Mesh.Grids: _x1, _x2, _x3\n\"\"\"\n InitStateBC\n\nSet the value at the boundary to match the `init_state_prognostic"
},
{
"path": "src/Atmos/Model/bc_moisture.jl",
"chars": 2546,
"preview": "abstract type MoistureBC end\n\n\"\"\"\n Impermeable() :: MoistureBC\n\nNo moisture flux.\n\"\"\"\nstruct Impermeable <: MoistureB"
},
{
"path": "src/Atmos/Model/bc_momentum.jl",
"chars": 3041,
"preview": "abstract type MomentumBC end\nabstract type MomentumDragBC end\n\n\"\"\"\n Impenetrable(drag::MomentumDragBC) :: MomentumBC\n"
},
{
"path": "src/Atmos/Model/bc_precipitation.jl",
"chars": 439,
"preview": "abstract type PrecipitationBC end\n\n\"\"\"\n OutflowPrecipitation() :: PrecipitationBC\n\nFree flux out of the domain.\n\"\"\"\ns"
},
{
"path": "src/Atmos/Model/bc_tracer.jl",
"chars": 409,
"preview": "abstract type TracerBC end\n\n\"\"\"\n ImpermeableTracer() :: TracerBC\n\nNo tracer diffusion across boundary\n\"\"\"\nstruct Impe"
},
{
"path": "src/Atmos/Model/boundaryconditions.jl",
"chars": 4526,
"preview": "using CLIMAParameters.Planet: cv_d, T_0\n\nexport InitStateBC\n\nexport AtmosBC,\n Impenetrable,\n FreeSlip,\n NoSlip,"
},
{
"path": "src/Atmos/Model/courant.jl",
"chars": 2008,
"preview": "using ..Mesh.Grids: Direction, HorizontalDirection, VerticalDirection\nusing ..TurbulenceClosures\n\nadvective_courant(m::A"
},
{
"path": "src/Atmos/Model/declare_prognostic_vars.jl",
"chars": 708,
"preview": "##### Prognostic variable\n\nexport Mass, Momentum, Energy, ρθ_liq_ice\nexport AbstractMoistureVariable, TotalMoisture, Liq"
},
{
"path": "src/Atmos/Model/energy.jl",
"chars": 1777,
"preview": "export AbstractEnergyModel, TotalEnergyModel, θModel\n#### Energy component in atmosphere model\nabstract type AbstractEne"
},
{
"path": "src/Atmos/Model/filters.jl",
"chars": 3094,
"preview": "export AtmosFilterPerturbations\nexport AtmosSpecificFilterPerturbations\n\nstruct AtmosFilterPerturbations{M} <: AbstractF"
},
{
"path": "src/Atmos/Model/get_prognostic_vars.jl",
"chars": 2206,
"preview": "##### Get prognostic variable list\n\nprognostic_vars(::TotalEnergyModel) = (Energy(),)\nprognostic_vars(::θModel) = (ρθ_li"
},
{
"path": "src/Atmos/Model/linear.jl",
"chars": 13718,
"preview": "using CLIMAParameters.Planet: R_d, cv_d, T_0, e_int_v0, e_int_i0\n\n\"\"\"\n linearized_air_pressure(ρ, ρe_tot, ρe_pot, ρq_"
},
{
"path": "src/Atmos/Model/linear_atmos_tendencies.jl",
"chars": 842,
"preview": "\n#####\n##### First order fluxes\n#####\n\n# Mass\neq_tends(::Mass, ::AtmosLinearModel, ::Flux{FirstOrder}) = (Advect(),)\n\n# "
},
{
"path": "src/Atmos/Model/linear_tendencies.jl",
"chars": 1600,
"preview": "##### Mass tendencies\n\n#####\n##### First order fluxes\n#####\n\nfunction flux(::Mass, ::Advect, lm::AtmosLinearModel, args)"
},
{
"path": "src/Atmos/Model/lsforcing.jl",
"chars": 1565,
"preview": "export LSForcingModel, NoLSForcing, HadGEMVertical\n\nabstract type LSForcingModel end\n\nvars_state(::LSForcingModel, ::Abs"
},
{
"path": "src/Atmos/Model/moisture.jl",
"chars": 4822,
"preview": "export AbstractMoistureModel, DryModel, EquilMoist, NonEquilMoist\n\n#### Moisture component in atmosphere model\nabstract "
},
{
"path": "src/Atmos/Model/multiphysics_types.jl",
"chars": 8455,
"preview": "##### Multi-physics types\n\nusing CLIMAParameters.Planet: T_freeze, cv_l\n\nusing CloudMicrophysics.Microphysics_0M\nusing C"
},
{
"path": "src/Atmos/Model/precipitation.jl",
"chars": 3593,
"preview": "#### Precipitation component in atmosphere model\nabstract type PrecipitationModel end\n\nexport PrecipitationModel, NoPrec"
},
{
"path": "src/Atmos/Model/problem.jl",
"chars": 1297,
"preview": "export AbstractAtmosProblem, AtmosProblem\n\ninclude(\"boundaryconditions.jl\")\n\nabstract type AbstractAtmosProblem <: Abstr"
},
{
"path": "src/Atmos/Model/prog_prim_conversion.jl",
"chars": 5104,
"preview": "####\n#### prognostic_to_primitive! and primitive_to_prognostic!\n####\n\n####\n#### Wrappers (entry point)\n####\n\n\"\"\"\n pro"
},
{
"path": "src/Atmos/Model/projections.jl",
"chars": 658,
"preview": "import ..BalanceLaws: projection\n\n# Zero-out vertical momentum tendencies based on compressibility\nfunction projection(p"
},
{
"path": "src/Atmos/Model/radiation.jl",
"chars": 823,
"preview": "export RadiationModel, NoRadiation\n\nabstract type RadiationModel end\n\nvars_state(::RadiationModel, ::AbstractStateType, "
},
{
"path": "src/Atmos/Model/reconstructions.jl",
"chars": 2309,
"preview": "using KernelAbstractions.Extras: @unroll\n\nexport HBFVReconstruction\n\nusing ..DGMethods.FVReconstructions: AbstractRecons"
},
{
"path": "src/Atmos/Model/ref_state.jl",
"chars": 7887,
"preview": "### Reference state\nusing DocStringExtensions\nusing Thermodynamics.TemperatureProfiles\nexport ReferenceState, NoReferenc"
},
{
"path": "src/Atmos/Model/tendencies_energy.jl",
"chars": 2392,
"preview": "##### Energy tendencies\n\n#####\n##### First order fluxes\n#####\n\nfunction flux(::Energy, ::Advect, atmos, args)\n @unpac"
},
{
"path": "src/Atmos/Model/tendencies_mass.jl",
"chars": 1232,
"preview": "##### Mass tendencies\n\n#####\n##### First order fluxes\n#####\n\nfunction flux(::Mass, ::Advect, atmos, args)\n return arg"
},
{
"path": "src/Atmos/Model/tendencies_moisture.jl",
"chars": 4405,
"preview": "##### Moisture tendencies\n\nexport CreateClouds\n\n#####\n##### First order fluxes\n#####\n\nfunction flux(::TotalMoisture, ::A"
},
{
"path": "src/Atmos/Model/tendencies_momentum.jl",
"chars": 3724,
"preview": "##### Momentum tendencies\n\nexport GeostrophicForcing\nexport Coriolis\nexport Gravity\nexport RayleighSponge\nusing CLIMAPar"
},
{
"path": "src/Atmos/Model/tendencies_precipitation.jl",
"chars": 1929,
"preview": "##### Precipitation tendencies\n\n#####\n##### First order fluxes\n#####\n\nfunction flux(::Rain, ::PrecipitationFlux, atmos, "
},
{
"path": "src/Atmos/Model/tendencies_tracers.jl",
"chars": 499,
"preview": "##### Moisture tendencies\n\n#####\n##### First order fluxes\n#####\n\nfunction flux(::Tracers{N}, ::Advect, atmos, args) wher"
},
{
"path": "src/Atmos/Model/thermo_states.jl",
"chars": 4217,
"preview": "#### thermodynamics\n\nexport new_thermo_state, recover_thermo_state\n\n\"\"\"\n new_thermo_state(atmos::AtmosModel, state::V"
},
{
"path": "src/Atmos/Model/thermo_states_anelastic.jl",
"chars": 2492,
"preview": "#### thermodynamics\n\nexport new_thermo_state_anelastic, recover_thermo_state_anelastic\n\n\"\"\"\n new_thermo_state_anelast"
},
{
"path": "src/Atmos/Model/tracers.jl",
"chars": 5043,
"preview": "# ## [Tracers](@id tracer-model)\n#\n#md # !!! note\n#md #\n#md # Usage: Enable tracers using a keyword argument in the "
},
{
"path": "src/Atmos/Parameterizations/GravityWaves/README.md",
"chars": 72,
"preview": "# ClimateMachine-atmos Gravity-waves\nParameterizations of gravity waves\n"
},
{
"path": "src/Atmos/Parameterizations/README.md",
"chars": 80,
"preview": "# ClimateMachine-atmos Parameterizations\nParameterizations for atmosphere model\n"
},
{
"path": "src/Atmos/Parameterizations/Radiation/README.md",
"chars": 85,
"preview": "# ClimateMachine-atmos Radiation\nParameterizations of atmospheric radiative transfer\n"
},
{
"path": "src/Atmos/TemperatureProfiles/TemperatureProfiles.jl",
"chars": 4489,
"preview": "module TemperatureProfiles\n\nusing DocStringExtensions\n\nexport TemperatureProfile,\n IsothermalProfile, DecayingTempera"
},
{
"path": "src/BalanceLaws/BalanceLaws.jl",
"chars": 1032,
"preview": "module BalanceLaws\n\nusing ..VariableTemplates\nusing StaticArrays\n\nexport BalanceLaw,\n vars_state,\n number_states,\n"
},
{
"path": "src/BalanceLaws/Problems.jl",
"chars": 833,
"preview": "module Problems\n\nexport AbstractProblem,\n init_state_prognostic!, init_state_auxiliary!, boundary_state!\n\n\"\"\"\n Abs"
},
{
"path": "src/BalanceLaws/boundaryconditions.jl",
"chars": 1519,
"preview": "# eventually boundary conditions should be a subtype of this\n# we don't enforce it currently to make the transition easi"
},
{
"path": "src/BalanceLaws/interface.jl",
"chars": 12153,
"preview": "#### Balance Law Interface\n\"\"\"\n abstract type BalanceLaw end\n\nAn abstract type representing a PDE balance law of the "
},
{
"path": "src/BalanceLaws/kernels.jl",
"chars": 3358,
"preview": "\n\"\"\"\n flux_first_order!(\n bl::BalanceLaw,\n flux::Grad,\n state::Vars,\n aux::Vars,\n "
},
{
"path": "src/BalanceLaws/prog_prim_conversion.jl",
"chars": 1756,
"preview": "# Add `Primitive` type to BalanceLaws, AtmosModel\n\n# Vars wrapper\nfunction prognostic_to_primitive!(\n bl::BalanceLaw,"
},
{
"path": "src/BalanceLaws/show_tendencies.jl",
"chars": 2070,
"preview": "##### Show tendencies\n\nexport show_tendencies\n\nusing PrettyTables\n\nformat_tend(tend_type) = \"$(nameof(typeof(tend_type))"
},
{
"path": "src/BalanceLaws/state_types.jl",
"chars": 2188,
"preview": "#### State types\n\nexport AbstractStateType,\n Prognostic,\n Primitive,\n Auxiliary,\n Gradient,\n GradientFlux"
},
{
"path": "src/BalanceLaws/sum_tendencies.jl",
"chars": 2714,
"preview": "##### Sum wrapper\n\nexport Σfluxes, Σsources\n\n\"\"\"\n flux\n\nAn individual flux.\nSee [`BalanceLaw`](@ref) for more info.\n\""
}
]
// ... and 470 more files (download for full content)
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