APIs

• inputs
  • inputs.rising_bubble
    • UserData
      • UserData.__init__()
    • sol_init()
• run_scripts
  • run_scripts.run
    • run_params
      • run_params.__init__()
      • run_params.N
      • run_params.tc
      • run_params.single_run()
      • run_params.queue_run()
      • run_params.restart_set()
      • run_params.restart_run()
  • run_scripts.test_suite
• src
  • src.data_assimilation
    • src.data_assimilation.blending
      • Blend
        • Blend.__init__()
        • Blend.criterion_init()
        • Blend.convert_p2n()
        • Blend.update_Sol()
        • Blend.update_p2n()
      • do_comp_to_psinc_conv()
      • do_psinc_to_comp_conv()
      • do_swe_to_lake_conv()
      • do_lake_to_swe_conv()
      • do_nonhydro_to_hydro_conv()
      • do_hydro_to_nonhydro_conv()
      • blending_before_timestep()
      • blending_after_timestep()
    • src.data_assimilation.etpf
      • da_interface()
      • analysis
        • analysis.__init__()
        • analysis.analyse()
        • analysis.state_vector()
        • analysis.get_ensemble_from_X()
    • src.data_assimilation.letkf
      • da_interface()
      • interpolation_func()
      • bin_func()
      • none_func()
      • analysis
        • analysis.__init__()
        • analysis.forward()
        • analysis.localisation()
        • analysis.analyse()
        • analysis.get_mean()
        • analysis.state_vector()
        • analysis.to_array()
        • analysis.debug()
      • prepare_rloc
        • prepare_rloc.__init__()
        • prepare_rloc.sort_locs()
        • prepare_rloc.analyse()
        • prepare_rloc.analyse_by_grid_type()
        • prepare_rloc.do_analysis
        • prepare_rloc.stack()
        • prepare_rloc.get_state()
        • prepare_rloc.get_obs()
        • prepare_rloc.get_state_in_obs_space()
        • prepare_rloc.get_bc_mask()
        • prepare_rloc.get_properties()
        • prepare_rloc.get_quantity()
        • prepare_rloc.get_loc_mat()
    • src.data_assimilation.localisation
      • rlocal_5pt()
      • rlocal_5pt_stencil()
    • src.data_assimilation.params
      • init
        • init.__init__()
        • init.gen_obs_sparse()
        • init.gen_obs_noise()
        • init.converter()
        • init.load_obs()
        • init.get_loc_mat()
        • init.update_dap()
        • init.noise_percentage
        • init.obs_attrs
        • init.da_times
        • init.loc_setter
        • init.sd_setter
    • src.data_assimilation.post_processing
      • interface()
    • src.data_assimilation.utils
      • ensemble
        • ensemble.__init__()
        • ensemble.initialise_members()
        • ensemble.set_members()
        • ensemble.ensemble_spreading()
        • ensemble.members()
        • ensemble.debug_im()
      • ensemble_inflation()
      • set_p2_nodes()
      • set_rhoY_cells()
      • boundary_mask()
      • sliding_window_view()
      • HSprojector_3t2D()
      • HSprojector_2t3D()
      • sparse_obs_selector()
      • obs_noiser()
  • src.dycore
    • src.dycore.discretisation
      • src.dycore.discretisation.grid
        • grid_init()
        • Grid
          • Grid.__init__()
        • SpaceDiscr
          • SpaceDiscr.ig
          • SpaceDiscr.ic
          • SpaceDiscr.stride
          • SpaceDiscr.dxyz
          • SpaceDiscr.__init__()
        • ElemSpaceDiscr
          • ElemSpaceDiscr.__init__()
          • ElemSpaceDiscr.flip()
          • ElemSpaceDiscr.get_p_indim()
        • NodeSpaceDiscr
          • NodeSpaceDiscr.__init__()
          • NodeSpaceDiscr.flip()
          • NodeSpaceDiscr.get_p_indim()
      • src.dycore.discretisation.time_update
        • data_init()
        • do()
    • src.dycore.physics
      • src.dycore.physics.gas_dynamics
        • src.dycore.physics.gas_dynamics.cfl
          • dynamic_timestep()
        • src.dycore.physics.gas_dynamics.eos
          • nonhydrostasy()
          • compressibility()
          • is_compressible()
          • is_nonhydrostatic()
          • rhoe()
          • synchronise_variables()
        • src.dycore.physics.gas_dynamics.explicit
          • advect()
          • explicit_step_and_flux()
          • advect_rk()
        • src.dycore.physics.gas_dynamics.numerical_flux
          • recompute_advective_fluxes()
          • hll_solver()
        • src.dycore.physics.gas_dynamics.recovery
          • do()
          • slopes()
          • limiters()
          • get_conservatives()
        • src.dycore.physics.gas_dynamics.thermodynamic
          • init
            • init.__init__()
      • src.dycore.physics.hydrostatics
        • column()
        • state()
        • initial_pressure()
      • src.dycore.physics.low_mach
        • src.dycore.physics.low_mach.laplacian
          • stencil_9pt()
          • lap2D_gather()
          • lap2D()
          • stencil_9pt_numba_test()
          • lap2D_numba_test()
          • lap2D_gather_new()
          • periodic()
          • stencil_27pt()
          • lap3D()
          • stencil_hs()
          • lapHS()
          • stencil_vs()
          • lapVS()
          • precon_diag_prepare()
          • stencil_3pt()
          • lap2D_exner()
          • stencil_5pt()
          • lap2D_5pt()
        • src.dycore.physics.low_mach.mpv
          • MPV
            • MPV.__init__()
            • MPV.squeezer()
        • src.dycore.physics.low_mach.second_projection
          • solver_counter
            • solver_counter.__init__()
          • euler_forward_non_advective()
          • euler_backward_non_advective_expl_part()
          • euler_backward_non_advective_impl_part()
          • correction_nodes()
          • operator_coefficients_nodes()
          • scale_wall_node_values()
          • grad_nodes_fft()
          • grad_nodes()
          • divergence_nodes()
          • rhs_from_p_old()
          • multiply_inverse_coriolis()
  • src.tests
    • src.tests.diagnostics
      • compare_sol
        • compare_sol.__init__()
        • compare_sol.update_targets()
        • compare_sol.test_do()
      • test_params
        • test_params.__init__()
    • src.tests.test_internal_long_wave
      • UserData
        • UserData.NSPEC
        • UserData.BUOY
        • UserData.grav
        • UserData.omega
        • UserData.R_gas
        • UserData.R_vap
        • UserData.Q_vap
        • UserData.gamma
        • UserData.i_gravity
        • UserData.i_coriolis
        • UserData.__init__()
        • UserData.scale_factor
        • UserData.h_ref
        • UserData.t_ref
        • UserData.T_ref
        • UserData.p_ref
        • UserData.rho_ref
        • UserData.u_ref
        • UserData.Nsq_ref
        • UserData.tout
        • UserData.stratification_function()
        • UserData.molly_function()
        • UserData.rhoe_method()
      • sol_init()
      • T_from_p_rho()
    • src.tests.test_lamb_wave
      • UserData
        • UserData.NSPEC
        • UserData.grav
        • UserData.omega
        • UserData.R_vap
        • UserData.Q_vap
        • UserData.gamma
        • UserData.N_ref
        • UserData.Cs
        • UserData.i_gravity
        • UserData.i_coriolis
        • UserData.__init__()
        • UserData.h_ref
        • UserData.t_ref
        • UserData.T_ref
        • UserData.p_ref
        • UserData.rho_ref
        • UserData.u_ref
        • UserData.R_gas
        • UserData.cp_gas
        • UserData.stratification_wrapper()
        • UserData.stratification_function()
        • UserData.rayleigh_bc_function()
        • UserData.forcing
          • UserData.forcing.__init__()
          • UserData.forcing.get_T_matrix()
          • UserData.forcing.eigenfunction()
          • UserData.forcing.dehatter()
      • sol_init()
    • src.tests.test_travelling_vortex
      • UserData
        • UserData.NSPEC
        • UserData.grav
        • UserData.omega
        • UserData.R_gas
        • UserData.R_vap
        • UserData.Q_vap
        • UserData.gamma
        • UserData.i_gravity
        • UserData.i_coriolis
        • UserData.__init__()
        • UserData.h_ref
        • UserData.t_ref
        • UserData.T_ref
        • UserData.p_ref
        • UserData.rho_ref
        • UserData.u_ref
        • UserData.Nsq_ref
        • UserData.tout
        • UserData.stratification_function()
        • UserData.rhoe_function()
      • sol_init()
      • T_from_p_rho()
  • src.utils
    • src.utils.io
      • init
        • init.__init__()
        • init.io_create_file()
        • init.write_all()
        • init.vortz()
        • init.vorty()
        • init.dpress_dim()
        • init.populate()
        • init.write_attrs()
        • init.write_da_attrs()
        • init.close_everything()
        • init.check_jar()
        • init.jar()
      • read_input
        • read_input.__init__()
        • read_input.get_data()
      • get_args()
      • sim_restart()
      • fn_gen()
      • mkdir_p()
      • init_logger()
    • src.utils.sim_params
      • global_constants
        • global_constants.__init__()
    • src.utils.user_data
      • UserDataInit
        • UserDataInit.__init__()
        • UserDataInit.compute_u_ref()
        • UserDataInit.compute_Msq()
        • UserDataInit.compute_gravity()
        • UserDataInit.compute_coriolis()
        • UserDataInit.compute_cp_gas()
        • UserDataInit.compute_rho_ref()
        • UserDataInit.compute_N_ref()
        • UserDataInit.compute_Cs()
        • UserDataInit.stratification_function()
        • UserDataInit.update_ud()
        • UserDataInit.R_gas
        • UserDataInit.T_ref
        • UserDataInit.grav
        • UserDataInit.h_ref
        • UserDataInit.t_ref
        • UserDataInit.omega
        • UserDataInit.gamm
        • UserDataInit.p_ref
  • src.vis
    • src.vis.plotting_tools
      • plotter
        • plotter.__init__()
        • plotter.set_axes()
        • plotter.set_cax_axes()
        • plotter.plot()
        • plotter.save_fig()
        • plotter.visualise()
      • animator_2D
        • animator_2D.__init__()
        • animator_2D.animate()
        • animator_2D.update_plot()
      • plotter_1d
        • plotter_1d.__init__()
        • plotter_1d.set_suptitle()
        • plotter_1d.set_x()
        • plotter_1d.get_ax()
        • plotter_1d.save_fig()
      • labels()
      • labels_increment()
      • swe_labels()
      • lake_labels()
      • swe_labels_increment()
      • short_labels()
    • src.vis.utils
      • test_case
        • test_case.__init__()
        • test_case.cb_suffix()
        • test_case.get_tag_dict()
        • test_case.get_debug_attrs()
        • test_case.get_filename()
        • test_case.get_path()
        • test_case.py_out()
        • test_case.get_arr()
        • test_case.spatially_averaged_rmse()
        • test_case.ensemble_spread()
        • test_case.probe_rmse()
        • test_case.get_ie1()
        • test_case.get_mean()
        • test_case.get_probe_loc()
        • test_case.get_ensemble()
        • test_case.get_time_series()
      • bin_func()
      • rmse()
      • get_diff()
      • spatially_averaged_rmse()
      • prt_time
        • prt_time.__init__()
        • prt_time.prtt()