SCHIMPY Toolset
The schimpy toolset is designed to help to pre- and post-process SCHISM simulations more easily. In particular, the tools allow you to specify things like boundaries and hydraulic structures using geophysical coordinates rather than node/element numbers … this can greatly simplify the work involved when the mesh is revised.
Please direct questions, suggestions or bug reports to Eli.Ateljevich@water.ca.gov or Kijin.Nam@water.ca.gov.
Usage
To use schimpy tools in a project:
import schimpy
Many schimpy utilities can be invoked as command line utilities and the most common of these is the prepare_schism command for the preprocessor invoked like this:
$ prepare_schism main_bay_delta.yaml
where main_bay_delta.yaml is the main yaml input file for your project.
Contents
- Installation
- Spatial data in SCHISM
- Pre-processing
- Working with SMS
- Model time
- Populating Elevation/Depth Data
- Creating hotstart
- Creating nudging
- Post-processing
- Evaluating Model Performance
- Using Python Pre-processing Script Programatically
- Module Documentation
- Command Line Tools
- Modules
- schimpy.base_io module
- schimpy.batch_metrics module
- schimpy.bctide module
- schimpy.bound_linear module
- schimpy.cencoos_download module
- schimpy.check_mesh_skewness module
- schimpy.clip_dems module
- schimpy.combine_consume module
- schimpy.combine_flux module
- schimpy.contour_smooth module
- schimpy.convert_linestrings module
- schimpy.convert_mesh module
- schimpy.convert_points module
- schimpy.convert_polygons module
- schimpy.convert_sav_class_to_number module
- schimpy.create_mesh_n_levels module
- schimpy.create_vgrid_lsc2 module
- schimpy.cruise module
- schimpy.cut_mesh module
- schimpy.download_hrrr module
- schimpy.embed_raster module
- schimpy.gaussian_quadrature module
GaussianQuadratureGaussianQuadrature.average()GaussianQuadrature.calculate_quadrature_points_and_weights()GaussianQuadrature.domain_size()GaussianQuadrature.integrate()GaussianQuadrature.jacobian_det()GaussianQuadrature.number_of_quadrature_points()GaussianQuadrature.quadrature_vector()GaussianQuadrature.shape()GaussianQuadrature.shape_derivative()GaussianQuadrature.values_at_quadrature_points()
GaussianQuadratureLine2GaussianQuadratureQuad4GaussianQuadratureTri3
- schimpy.gen_elev2d module
- schimpy.geo_tools module
- schimpy.gr3 module
- schimpy.grid_opt module
GridOptimizerGridOptimizer.assemble_element_matrix()GridOptimizer.assemble_face_matrix()GridOptimizer.build_boundary_equations()GridOptimizer.build_global_matrix_and_vector()GridOptimizer.calculate_depth_at_element_quad_points()GridOptimizer.calculate_depth_at_face_quad_points()GridOptimizer.calculate_edge_lengths()GridOptimizer.calculate_element_areas()GridOptimizer.calculate_element_volumes_w_dem()GridOptimizer.calculate_face_areas_w_dem()GridOptimizer.calculate_max_elevation_in_balls()GridOptimizer.calculate_reference_surface()GridOptimizer.calculate_reference_surface_at_face_quadarture_points()GridOptimizer.calculate_reference_surface_maximum()GridOptimizer.calculate_total_number_of_quadrature_points()GridOptimizer.calculate_values_at_element_quadarture_points()GridOptimizer.calculate_values_at_face_quadarture_points()GridOptimizer.collect_edges()GridOptimizer.collect_element_quadrature_points_for_dem()GridOptimizer.collect_face_quadrature_points_for_dem()GridOptimizer.count_boundary_equations()GridOptimizer.get_dem_elevation()GridOptimizer.integrate_over_edges()GridOptimizer.integrate_over_elements()GridOptimizer.optimize()GridOptimizer.select_solver()GridOptimizer.show_parameters()
create_arg_parser()fprime()grid_opt_with_args()init_logger()main()object_func()
- schimpy.hotstart_inventory module
- schimpy.hrr3 module
- schimpy.interp_2d module
- schimpy.interpolate_structure module
- schimpy.laplace_smooth_data module
- schimpy.lsc2 module
- schimpy.material_poly module
- schimpy.merge_th module
- schimpy.metricsplot module
- schimpy.model_time module
- schimpy.nml module
- schimpy.nudging module
NudgingNudging.concatenate_nudge()Nudging.construct_weights()Nudging.create_nudging()Nudging.create_region_nudging()Nudging.gaussian_weights()Nudging.gen_nudge_3dfield()Nudging.gen_nudge_obs()Nudging.gen_region_weight()Nudging.get_nudging_comb()Nudging.in_vertices()Nudging.mesh_gpdNudging.organize_nudging()Nudging.plot()Nudging.read_data()Nudging.read_yaml()Nudging.reorder_variables()Nudging.signa()Nudging.z
create_arg_parser()main()write_to_log()
- schimpy.param module
ParamsParams.adjust_dt()Params.copy()Params.diff()Params.get_baro()Params.get_hotstart_freq()Params.get_interval()Params.get_nc_out_freq()Params.get_nc_stack()Params.get_run_start()Params.get_station_out_freq()Params.hotstart_freqParams.nc_out_freqParams.nc_stackParams.process_default()Params.run_startParams.searchfor()Params.sections()Params.set_hotstart_freq()Params.set_interval()Params.set_nc_out_freq()Params.set_nc_stack()Params.set_run_start()Params.set_station_out_freq()Params.station_out_freqParams.to_dataframe()Params.update()Params.validate()Params.write()
param_from_template()read_params()test_param()
- schimpy.params module
CoreHydroOutputHydroOutput.air_pressureHydroOutput.air_temperatureHydroOutput.barotropic_pres_grad_xyHydroOutput.bottom_stress_xyHydroOutput.depth_avg_vel_xyHydroOutput.diffusivityHydroOutput.downward_longwaveHydroOutput.dry_flag_nodeHydroOutput.elevationHydroOutput.evaporation_rateHydroOutput.horizontal_side_vel_xyHydroOutput.horizontal_vel_xyHydroOutput.latent_heatHydroOutput.mixing_lengthHydroOutput.precipitation_rateHydroOutput.salinityHydroOutput.salinity_at_elementHydroOutput.sensible_heatHydroOutput.solar_radiationHydroOutput.specific_humidityHydroOutput.temperatureHydroOutput.temperature_at_elementHydroOutput.total_heatHydroOutput.turbulent_kinetic_enerHydroOutput.upward_longwaveHydroOutput.vertical_vel_at_elementHydroOutput.vertical_velocityHydroOutput.viscosityHydroOutput.water_densityHydroOutput.wind_speed_xyHydroOutput.wind_stress_xyHydroOutput.z_coordinates
OptOpt.cur_wwmOpt.dramp_ssOpt.eos_aOpt.eos_bOpt.fwvor_advxy_stokesOpt.fwvor_advz_stokesOpt.fwvor_breakingOpt.fwvor_gradpressOpt.fwvor_streamingOpt.fwvor_wvegOpt.fwvor_wveg_NLOpt.h1_bccOpt.h2_bccOpt.hw_depthOpt.hw_ratioOpt.iadjust_mass_consv0Opt.ieos_presOpt.ieos_typeOpt.if_sourceOpt.inunflOpt.inv_atm_bndOpt.ipre2Opt.isavOpt.iunder_deepOpt.iwblOpt.nstep_iceOpt.rho0Opt.shwOpt.slr_rateOpt.turbinjOpt.vclose_surf_fracOpt.wafo_obcramp
OutControlsParamsSchoutTracerGenOutputWindWaveOutputbuild_iof_dict()coerce_to_type()create_params()get_type_dict()get_value_dict()
- schimpy.plot_default_formats module
- schimpy.prepare_schism module
- schimpy.priority_queue module
- schimpy.profile_plot module
- schimpy.raster_to_nodes module
- schimpy.read_output_xyt module
- schimpy.schism_hotstart module
SCHISMHotstartVariableFieldVariableField.GenerateField()VariableField.create_dataarray()VariableField.define_new_grid()VariableField.elem2node_values()VariableField.extrude_casts()VariableField.get_grid()VariableField.get_key()VariableField.get_value()VariableField.hotstart_nc()VariableField.initializer_options()VariableField.interp_from_mesh()VariableField.map_to_3D()VariableField.node2elem_values()VariableField.obs_points()VariableField.patch_init()VariableField.patch_initializer_options()VariableField.schout_nc()VariableField.simple_trend()VariableField.text_init()VariableField.var_centering()
create_arg_parser()describe_tracers()hotstarthotstart_to_outputnc()main()num()project_mesh()read_hotstart()read_param_nml()
- schimpy.schism_input module
- schimpy.schism_linestring module
- schimpy.schism_mesh module
BoundaryTypeSchismMeshSchismMesh.add_boundary()SchismMesh.areas()SchismMesh.boundariesSchismMesh.build_z()SchismMesh.centroids()SchismMesh.clear_boundaries()SchismMesh.edge_len()SchismMesh.fill_land_and_island_boundaries()SchismMesh.fill_open_boundaries()SchismMesh.find_two_neighboring_node_paths()SchismMesh.get_centers_of_elements()SchismMesh.get_centers_of_sides()SchismMesh.get_coordinates_3d()SchismMesh.merged_mesh()SchismMesh.n_boundaries()SchismMesh.n_total_boundary_nodes()SchismMesh.n_vert_levelsSchismMesh.plot_edges()SchismMesh.plot_elems()SchismMesh.plot_mesh_boundary()SchismMesh.plot_nodes()SchismMesh.plot_open_boundaries()SchismMesh.to_geopandas()SchismMesh.trim_to_left_of_mesh()SchismMesh.vmeshSchismMesh.z
read_mesh()write_mesh()
- schimpy.schism_polygon module
- schimpy.schism_setup module
SchismSetupSchismSetup.adopt_new_mesh()SchismSetup.apply_linestring_ops()SchismSetup.apply_polygons()SchismSetup.creart_sources_from_user_input()SchismSetup.create_flux_regions()SchismSetup.create_node_partitioning()SchismSetup.create_open_boundaries()SchismSetup.create_prop_partitioning()SchismSetup.create_source_sink_in()SchismSetup.create_structures()SchismSetup.elements_on_linestring()SchismSetup.get_closest_node_i_from_new_mesh()SchismSetup.inputSchismSetup.interpolate_tide()SchismSetup.load()SchismSetup.meshSchismSetup.modify_depth()SchismSetup.reorder_open_boundaries()SchismSetup.trim_to_left_of_mesh()SchismSetup.write_hgrid()SchismSetup.write_hgrid_ll()SchismSetup.write_structures()
check_and_suggest()check_similarity()create_schism_setup()ensure_outdir()load_schism()
- schimpy.schism_source module
- schimpy.schism_sources_sinks module
- schimpy.schism_structure module
- schimpy.schism_vertical_mesh module
- schimpy.schism_yaml module
- schimpy.separate_species module
- schimpy.simulation_timing module
- schimpy.small_areas module
- schimpy.sms2gr3 module
- schimpy.split_quad module
- schimpy.stacked_dem_fill module
- schimpy.station module
convert_db_station_in()convert_stations()create_arg_parser()example()flux_stations_from_yaml()main()merge_station_subloc()read_flux_out()read_obs_links()read_pointstrings()read_staout()read_station_dbase()read_station_in()read_station_out()read_station_shp()read_station_subloc()staout_name()station_names_from_file()station_subset()station_subset_multidir()u()write_pointstrings()write_station_in()write_station_shp()
- schimpy.subset_schism_output module
- schimpy.three_point_linear_norm module
- schimpy.trimesh module
BoundaryTypesEdgeTypesTriMeshTriMesh.add_boundary()TriMesh.allocate()TriMesh.build_edgecenters()TriMesh.build_edges_from_elems()TriMesh.deepcopy()TriMesh.edgesTriMesh.element2edges()TriMesh.elemsTriMesh.find_closest_elems()TriMesh.find_closest_nodes()TriMesh.find_elem()TriMesh.find_elem_with_tolerance()TriMesh.find_nodes_in_box()TriMesh.get_edges_from_node()TriMesh.get_elems_i_from_node()TriMesh.get_neighbor_nodes()TriMesh.is_elem_on_boundary()TriMesh.n_edges()TriMesh.n_elems()TriMesh.n_nodes()TriMesh.nodesTriMesh.set_elem()TriMesh.set_node()TriMesh.shortest_path()TriMesh.trim_to_left()
enum()
- schimpy.triquadmesh module
BoundaryTypeEdgeTypeNodeTypeTriQuadMeshTriQuadMesh.add_boundary()TriQuadMesh.allocate()TriQuadMesh.build_edgecenters()TriQuadMesh.build_edges_from_elems()TriQuadMesh.build_elem_balls()TriQuadMesh.compare()TriQuadMesh.edgesTriQuadMesh.elem()TriQuadMesh.element2edges()TriQuadMesh.elemsTriQuadMesh.find_closest_elems()TriQuadMesh.find_closest_nodes()TriQuadMesh.find_edge()TriQuadMesh.find_elem()TriQuadMesh.find_intersecting_elems_with_line()TriQuadMesh.find_neighbors_on_segment()TriQuadMesh.find_nodes_in_box()TriQuadMesh.get_edges_from_node()TriQuadMesh.get_elems_i_from_node()TriQuadMesh.get_neighbor_nodes()TriQuadMesh.is_elem_on_boundary()TriQuadMesh.mark_elem_deleted()TriQuadMesh.n_edges()TriQuadMesh.n_elems()TriQuadMesh.n_nodes()TriQuadMesh.node()TriQuadMesh.node2elemsTriQuadMesh.nodesTriQuadMesh.renumber()TriQuadMesh.set_elem()TriQuadMesh.set_node()TriQuadMesh.shortest_path()TriQuadMesh.trim_elems()
enum()
- schimpy.unit_conversions module
- schimpy.vgrid_opt2 module
- schimpy.write_ts module
- History
- License
- Contributing
- Authors
- Project README