pylag package

Subpackages

• pylag.parallel package
  • Submodules
    • pylag.parallel.main module
      • main()
    • pylag.parallel.mediator module
      • MPIMediator
    • pylag.parallel.model_factory module
      • get_model()
    • pylag.parallel.simulator module
      • Simulator
      • TraceSimulator
      • get_simulator()
  • Module contents
    • pylag.parallel
• pylag.processing package
  • Submodules
    • pylag.processing.animation module
      • Animation
      • ParticleTrajectoryAnimation
    • pylag.processing.coordinate module
      • british_national_grid_to_lonlat()
      • check_valid_zone()
      • get_epsg_code()
      • get_zone_letter()
      • get_zone_number()
      • lonlat_decimal_from_degminsec()
      • lonlat_decimal_from_degminsec_wco()
      • lonlat_from_utm()
      • to_ndarray()
      • utm_from_lonlat()
    • pylag.processing.ensemble module
      • get_probability_density_1D()
      • get_probability_density_2D()
    • pylag.processing.fvcom module
      • get_rmse()
    • pylag.processing.gotm module
      • get_rmse()
    • pylag.processing.input module
      • create_initial_positions_file_multi_group()
      • create_initial_positions_file_single_group()
    • pylag.processing.ncview module
      • Viewer
    • pylag.processing.plot module
      • ArakawaAPlotter
      • ArakawaCPlotter
      • FVCOMPlotter
      • GOTMPlotter
      • PyLagPlotter
      • cm2inch()
      • colourmap()
      • create_cbar_ax()
      • create_figure()
    • pylag.processing.release_zone module
      • ReleaseZone
      • create_release_zone()
      • create_release_zones_along_cord()
      • create_release_zones_around_shape()
    • pylag.processing.utils module
      • get_file_list()
      • get_grid_bands()
      • get_time_index()
      • round_time()
  • Module contents
    • pylag.processing
• pylag.regrid package
  • Submodules
    • pylag.regrid.regridder module
      • Regridder
  • Module contents
    • pylag.regrid

Submodules

• pylag.arakawa_a_data_reader module
  • ArakawaADataReader
    • ArakawaADataReader.get_grid_names()
    • ArakawaADataReader.get_xmin()
    • ArakawaADataReader.get_ymin()
    • ArakawaADataReader.read_data()
    • ArakawaADataReader.setup_data_access()
• pylag.atmosphere_data_reader module
  • AtmosphereDataReader
    • AtmosphereDataReader.get_grid_names()
    • AtmosphereDataReader.read_data()
    • AtmosphereDataReader.setup_data_access()
• pylag.bio_model module
  • BioModel
• pylag.boundary_conditions module
  • AbsBotVertBoundaryConditionCalculator
  • AbsorbingHorizBoundaryConditionCalculator
  • HorizBoundaryConditionCalculator
    • HorizBoundaryConditionCalculator.apply_wrapper()
  • RefHorizCartesianBoundaryConditionCalculator
  • RefHorizGeographicBoundaryConditionCalculator
  • RefVertBoundaryConditionCalculator
  • RestoringHorizBoundaryConditionCalculator
  • VertBoundaryConditionCalculator
    • VertBoundaryConditionCalculator.apply_wrapper()
  • get_horiz_boundary_condition_calculator()
  • get_vert_boundary_condition_calculator()
• pylag.composite_data_reader module
  • CompositeDataReader
    • CompositeDataReader.get_grid_names()
    • CompositeDataReader.get_xmin()
    • CompositeDataReader.get_ymin()
    • CompositeDataReader.read_data()
    • CompositeDataReader.setup_data_access()
• pylag.configuration module
  • get_config()
• pylag.data_reader module
  • DataReader
    • DataReader.find_host_using_global_search_wrapper()
    • DataReader.find_host_using_local_search_wrapper()
    • DataReader.find_host_wrapper()
    • DataReader.find_nearest_wet_host_wrapper()
    • DataReader.get_boundary_intersection_wrapper()
    • DataReader.get_environmental_variable_wrapper()
    • DataReader.get_grid_names()
    • DataReader.get_horizontal_eddy_diffusivity_derivative_wrapper()
    • DataReader.get_horizontal_eddy_diffusivity_wrapper()
    • DataReader.get_horizontal_velocity_wrapper()
    • DataReader.get_surface_stokes_drift_velocity_wrapper()
    • DataReader.get_ten_meter_wind_velocity_wrapper()
    • DataReader.get_velocity_wrapper()
    • DataReader.get_vertical_eddy_diffusivity_derivative_wrapper()
    • DataReader.get_vertical_eddy_diffusivity_wrapper()
    • DataReader.get_xmin()
    • DataReader.get_ymin()
    • DataReader.get_zmax_wrapper()
    • DataReader.get_zmin_wrapper()
    • DataReader.is_wet_wrapper()
    • DataReader.read_data()
    • DataReader.set_default_location_wrapper()
    • DataReader.set_local_coordinates_wrapper()
    • DataReader.set_vertical_grid_vars_wrapper()
    • DataReader.setup_data_access()
• pylag.data_types_python module
• pylag.datetime_reader module
  • DateTimeReader
    • DateTimeReader.get_datetime()
  • DefaultDateTimeReader
    • DefaultDateTimeReader.get_datetime()
  • FVCOMDateTimeReader
    • FVCOMDateTimeReader.get_datetime()
  • get_datetime_reader()
• pylag.delta module
• pylag.exceptions module
  • PyLagAttributeError
  • PyLagException
  • PyLagOutOfBoundsError
  • PyLagRuntimeError
  • PyLagTypeError
  • PyLagValueError
• pylag.file_reader module
  • DatasetReader
    • DatasetReader.read_dataset()
  • DiskFileNameReader
    • DiskFileNameReader.get_file_names()
  • FileNameReader
    • FileNameReader.get_file_names()
  • FileReader
    • FileReader.compute_time_delta_between_datasets()
    • FileReader.get_dimension_variable()
    • FileReader.get_grid_variable()
    • FileReader.get_grid_variable_dimensions()
    • FileReader.get_mask_at_last_time_index()
    • FileReader.get_mask_at_next_time_index()
    • FileReader.get_time_at_last_time_index()
    • FileReader.get_time_at_next_time_index()
    • FileReader.get_time_dependent_variable_at_last_time_index()
    • FileReader.get_time_dependent_variable_at_next_time_index()
    • FileReader.get_variable_dimensions()
    • FileReader.get_variable_shape()
    • FileReader.setup_data_access()
    • FileReader.update_reading_frames()
  • NetCDFDatasetReader
    • NetCDFDatasetReader.read_dataset()
• pylag.fvcom_data_reader module
  • FVCOMDataReader
    • FVCOMDataReader.get_grid_names()
    • FVCOMDataReader.get_xmin()
    • FVCOMDataReader.get_ymin()
    • FVCOMDataReader.read_data()
    • FVCOMDataReader.setup_data_access()
  • sigma_to_z()
• pylag.gotm_data_reader module
  • GOTMDataReader
    • GOTMDataReader.get_xmin()
    • GOTMDataReader.get_ymin()
    • GOTMDataReader.read_data()
    • GOTMDataReader.setup_data_access()
• pylag.grid_metrics module
  • create_arakawa_a_grid_metrics_file()
  • create_fvcom_grid_metrics_file()
• pylag.interpolation module
  • CubicSpline1DInterpolator
  • Interpolator
  • Linear1DInterpolator
  • get_euclidian_distance()
  • get_interpolator()
  • get_linear_fraction()
  • interpolate_within_element_wrapper()
  • linear_interp()
• pylag.main module
  • main()
• pylag.math module
  • angle_between_two_unit_vectors_wrapper()
  • area_of_a_spherical_triangle_wrapper()
  • area_of_a_triangle_wrapper()
  • cartesian_to_geographic_coords_python()
  • cartesian_to_geographic_coords_wrapper()
  • cartesian_to_sigma_coords()
  • det_second_order_wrapper()
  • det_third_order_wrapper()
  • euclidian_norm_wrapper()
  • geographic_to_cartesian_coords_python()
  • geographic_to_cartesian_coords_wrapper()
  • get_intersection_point_in_geographic_coordinates_wrapper()
  • get_intersection_point_wrapper()
  • great_circle_arc_segments_intersect_wrapper()
  • haversine()
  • inner_product_three_wrapper()
  • inner_product_two_wrapper()
  • rotate_axes_wrapper()
  • rotate_x_wrapper()
  • rotate_y_wrapper()
  • rotate_z_wrapper()
  • sigma_to_cartesian_coords()
  • unit_vector_wrapper()
  • vector_product_wrapper()
• pylag.mediator module
  • Mediator
    • Mediator.get_dimension_variable()
    • Mediator.get_grid_variable()
    • Mediator.get_grid_variable_dimensions()
    • Mediator.get_mask_at_last_time_index()
    • Mediator.get_mask_at_next_time_index()
    • Mediator.get_time_at_last_time_index()
    • Mediator.get_time_at_next_time_index()
    • Mediator.get_time_dependent_variable_at_last_time_index()
    • Mediator.get_time_dependent_variable_at_next_time_index()
    • Mediator.get_variable_dimensions()
    • Mediator.get_variable_shape()
    • Mediator.setup_data_access()
    • Mediator.update_reading_frames()
  • SerialMediator
    • SerialMediator.get_dimension_variable()
    • SerialMediator.get_grid_variable()
    • SerialMediator.get_grid_variable_dimensions()
    • SerialMediator.get_mask_at_last_time_index()
    • SerialMediator.get_mask_at_next_time_index()
    • SerialMediator.get_time_at_last_time_index()
    • SerialMediator.get_time_at_next_time_index()
    • SerialMediator.get_time_dependent_variable_at_last_time_index()
    • SerialMediator.get_time_dependent_variable_at_next_time_index()
    • SerialMediator.get_variable_dimensions()
    • SerialMediator.get_variable_shape()
    • SerialMediator.setup_data_access()
    • SerialMediator.update_reading_frames()
• pylag.mock module
  • MockAtmosphereDataReader
  • MockHorizontalEddyDiffusivityDataReader
  • MockOPTModelDataReader
    • MockOPTModelDataReader.get_xmin()
    • MockOPTModelDataReader.get_ymin()
  • MockOceanDataReader
  • MockOneDNumMethod
    • MockOneDNumMethod.step()
  • MockThreeDNumMethod
    • MockThreeDNumMethod.step()
  • MockTwoDNumMethod
    • MockTwoDNumMethod.step()
  • MockVelocityDataReader
    • MockVelocityDataReader.get_position_analytic()
    • MockVelocityDataReader.get_velocity_analytic()
  • MockVelocityEddyDiffusivityDataReader
    • MockVelocityEddyDiffusivityDataReader.M
    • MockVelocityEddyDiffusivityDataReader.get_concentration_analytic()
  • MockVerticalDiffusivityDataReader
    • MockVerticalDiffusivityDataReader.get_vertical_eddy_diffusivity_analytic()
    • MockVerticalDiffusivityDataReader.get_vertical_eddy_diffusivity_derivative_analytic()
  • MockWavesDataReader
• pylag.model module
  • OPTModel
    • OPTModel.get_diagnostics()
    • OPTModel.get_grid_names()
    • OPTModel.get_particle_data()
    • OPTModel.read_input_data()
    • OPTModel.seed()
    • OPTModel.set_particle_data()
    • OPTModel.setup_input_data_access()
    • OPTModel.update()
• pylag.model_factory module
  • get_model()
• pylag.mortality module
  • FixedTimeMortalityCalculator
  • MortalityCalculator
    • MortalityCalculator.apply_wrapper()
    • MortalityCalculator.set_initial_particle_properties_wrapper()
  • ProbabilisticMortalityCalculator
  • get_mortality_calculator()
• pylag.netcdf_logger module
  • NetCDFLogger
    • NetCDFLogger.close()
    • NetCDFLogger.sync()
    • NetCDFLogger.write()
    • NetCDFLogger.write_group_ids()
• pylag.numerics module
  • AdvDiffMilstein1DItMethod
  • AdvDiffMilstein3DItMethod
  • AdvRK42DItMethod
  • AdvRK43DItMethod
  • DiffConst2DItMethod
  • DiffEuler1DItMethod
  • DiffMilstein1DItMethod
  • DiffMilstein2DItMethod
  • DiffMilstein3DItMethod
  • DiffNaive1DItMethod
  • DiffNaive2DItMethod
  • DiffVisser1DItMethod
  • EulerParticleStateNumMethod
  • ItMethod
  • NumMethod
    • NumMethod.step_wrapper()
  • OS0NumMethod
  • OS1NumMethod
  • ParticleStateNumMethod
  • StdNumMethod
  • TestNumMethod
  • get_adv_iterative_method()
  • get_bio_time_step()
  • get_diff_iterative_method()
  • get_global_time_step()
  • get_iterative_method()
  • get_num_method()
  • get_particle_state_num_method()
  • get_time_direction()
• pylag.parameters module
• pylag.particle_cpp_wrapper module
  • ParticleSmartPtr
    • ParticleSmartPtr.age
    • ParticleSmartPtr.fixed_depth
    • ParticleSmartPtr.fixed_height
    • ParticleSmartPtr.get_all_boolean_flags()
    • ParticleSmartPtr.get_all_diagnostic_variables()
    • ParticleSmartPtr.get_all_host_horizontal_elems()
    • ParticleSmartPtr.get_all_parameters()
    • ParticleSmartPtr.get_all_state_variables()
    • ParticleSmartPtr.get_boolean_flag()
    • ParticleSmartPtr.get_diagnostic_variable()
    • ParticleSmartPtr.get_host_horizontal_elem()
    • ParticleSmartPtr.get_parameter()
    • ParticleSmartPtr.get_particle_data()
    • ParticleSmartPtr.get_phi()
    • ParticleSmartPtr.get_state_variable()
    • ParticleSmartPtr.in_bottom_boundary_layer
    • ParticleSmartPtr.in_domain
    • ParticleSmartPtr.in_surface_boundary_layer
    • ParticleSmartPtr.is_alive
    • ParticleSmartPtr.is_beached
    • ParticleSmartPtr.k_layer
    • ParticleSmartPtr.k_lower_layer
    • ParticleSmartPtr.k_upper_layer
    • ParticleSmartPtr.land_boundary_encounters
    • ParticleSmartPtr.omega_interfaces
    • ParticleSmartPtr.omega_layers
    • ParticleSmartPtr.restore_to_fixed_depth
    • ParticleSmartPtr.restore_to_fixed_height
    • ParticleSmartPtr.set_age()
    • ParticleSmartPtr.set_all_boolean_flags()
    • ParticleSmartPtr.set_all_diagnostic_variables()
    • ParticleSmartPtr.set_all_host_horizontal_elems()
    • ParticleSmartPtr.set_all_parameters()
    • ParticleSmartPtr.set_all_phis()
    • ParticleSmartPtr.set_all_state_variables()
    • ParticleSmartPtr.set_boolean_flag()
    • ParticleSmartPtr.set_diagnostic_variable()
    • ParticleSmartPtr.set_host_horizontal_elem()
    • ParticleSmartPtr.set_parameter()
    • ParticleSmartPtr.set_phi()
    • ParticleSmartPtr.set_state_variable()
    • ParticleSmartPtr.status
    • ParticleSmartPtr.x1
    • ParticleSmartPtr.x2
    • ParticleSmartPtr.x3
  • to_string_wrapper()
• pylag.particle_initialisation module
  • ASCIIInitialParticleStateReader
    • ASCIIInitialParticleStateReader.get_particle_data()
  • InitialParticleStateReader
    • InitialParticleStateReader.get_particle_data()
  • RestartInitialParticleStateReader
    • RestartInitialParticleStateReader.get_particle_data()
  • get_initial_particle_state_reader()
• pylag.position_modifier module
  • CartesianPositionModifier
  • GeographicPositionModifier
  • PositionModifier
  • get_position_modifier()
• pylag.random module
  • Pymt19937
  • gauss()
  • get_seed()
  • seed()
  • uniform()
• pylag.restart module
  • RestartFileCreator
    • RestartFileCreator.create()
• pylag.roms_data_reader module
  • ROMSDataReader
    • ROMSDataReader.compute_depths()
    • ROMSDataReader.get_grid_names()
    • ROMSDataReader.get_xmin()
    • ROMSDataReader.get_ymin()
    • ROMSDataReader.read_data()
    • ROMSDataReader.rotate_vector()
    • ROMSDataReader.setup_data_access()
    • ROMSDataReader.u_to_rho()
    • ROMSDataReader.v_to_rho()
• pylag.settling module
  • ConstantSettlingVelocityCalculator
  • DelayedSettlingVelocityCalculator
  • SettlingVelocityCalculator
    • SettlingVelocityCalculator.init_particle_settling_velocity_wrapper()
    • SettlingVelocityCalculator.set_particle_settling_velocity_wrapper()
  • get_settling_velocity_calculator()
• pylag.simulator module
  • Simulator
    • Simulator.run()
  • TraceSimulator
    • TraceSimulator.run()
  • get_simulator()
• pylag.spline_cpp_wrapper module
  • SplineWrapper
• pylag.stokes_drift module
  • StokesDriftCalculator
    • StokesDriftCalculator.get_velocity_wrapper()
  • SurfaceStokesDriftCalculator
  • get_stokes_drift_calculator()
• pylag.time_manager module
  • TimeManager
    • TimeManager.create_restart_file()
    • TimeManager.current_release
    • TimeManager.datetime_current
    • TimeManager.datetime_end
    • TimeManager.datetime_start
    • TimeManager.new_simulation()
    • TimeManager.number_of_particle_releases
    • TimeManager.sync_data_to_disk()
    • TimeManager.time
    • TimeManager.time_end
    • TimeManager.time_step
    • TimeManager.update_current_time()
    • TimeManager.write_output_to_file()
• pylag.unstructured module
  • Grid
    • Grid.find_host_using_global_search_wrapper()
    • Grid.find_host_using_local_search_wrapper()
    • Grid.find_host_using_particle_tracing_wrapper()
    • Grid.get_boundary_intersection_wrapper()
    • Grid.get_element_area_wrapper()
    • Grid.get_grad_phi_wrapper()
    • Grid.get_phi()
    • Grid.interpolate_in_space_wrapper()
    • Grid.interpolate_in_time_and_space_2D_wrapper()
    • Grid.interpolate_in_time_and_space_wrapper()
    • Grid.set_default_location_wrapper()
    • Grid.set_local_coordinates_wrapper()
    • Grid.shepard_interpolation_wrapper()
  • UnstructuredCartesianGrid
    • UnstructuredCartesianGrid.get_phi()
  • UnstructuredGeographicGrid
    • UnstructuredGeographicGrid.get_phi()
  • get_unstructured_grid()
• pylag.utils module
  • round_time()
• pylag.variable_library module
  • get_coordinate_variable_name()
  • get_data_type()
  • get_integer_type()
  • get_invalid_value()
  • get_long_name()
  • get_real_type()
  • get_units()
• pylag.velocity_aggregator module
  • VelocityAggregator
    • VelocityAggregator.get_velocity_wrapper()
• pylag.version module
• pylag.waves_data_reader module
  • WavesDataReader
    • WavesDataReader.get_grid_names()
    • WavesDataReader.read_data()
    • WavesDataReader.setup_data_access()
• pylag.windage module
  • WindageCalculator
    • WindageCalculator.get_velocity_wrapper()
  • ZeroDeflectionWindageCalculator
  • get_windage_calculator()

Module contents

PyLag

A particle tracking tool for marine applications.

Address: Plymouth Marine Laboratory Prospect Place, The Hoe Plymouth, PL1 3DH, UK

Conact: James Clark (Plymouth Marine Laboratory). Email: jcl@pml.ac.uk