ocean

Ocean()

The collection of all test case for the MPAS-Ocean core

Test Groups

baroclinic_channel

BaroclinicChannel(mpas_core)	A test group for baroclinic channel test cases
configure(resolution, config)	Modify the configuration options for one of the baroclinic test cases
decomp_test.DecompTest(test_group, resolution)	A decomposition test case for the baroclinic channel test group, which makes sure the model produces identical results on 1 and 4 cores.
decomp_test.DecompTest.configure()	Modify the configuration options for this test case.
decomp_test.DecompTest.run()	Run each step of the test case.
default.Default(test_group, resolution)	The default test case for the baroclinic channel test group simply creates the mesh and initial condition, then performs a short forward run on 4 cores.
default.Default.configure()	Modify the configuration options for this test case.
default.Default.run()	Run each step of the test case.
restart_test.RestartTest(test_group, resolution)	A restart test case for the baroclinic channel test group, which makes sure the model produces identical results with one longer run and two shorter runs with a restart in between.
restart_test.RestartTest.configure()	Modify the configuration options for this test case.
restart_test.RestartTest.run()	Run each step of the test case.
rpe_test.RpeTest(test_group, resolution)	The reference potential energy (RPE) test case for the baroclinic channel test group performs a 20-day integration of the model forward in time at 5 different values of the viscosity at the given resolution.
rpe_test.RpeTest.configure()	Modify the configuration options for this test case.
rpe_test.RpeTest.run()	Run each step of the test case.
rpe_test.analysis.Analysis(test_case, ...)	A step for plotting the results of a series of RPE runs in the baroclinic channel test group
rpe_test.analysis.Analysis.setup()	Set up the test case in the work directory, including downloading any dependencies.
rpe_test.analysis.Analysis.run()	Run this step of the test case
threads_test.ThreadsTest(test_group, resolution)	A thread test case for the baroclinic channel test group, which makes sure the model produces identical results with 1 and 2 threads.
threads_test.ThreadsTest.configure()	Modify the configuration options for this test case.
threads_test.ThreadsTest.run()	Run each step of the test case.
forward.Forward(test_case, resolution[, ...])	A step for performing forward MPAS-Ocean runs as part of baroclinic channel test cases.
forward.Forward.setup()	Set up the test case in the work directory, including downloading any dependencies.
forward.Forward.run()	Run this step of the test case
initial_state.InitialState(test_case, resolution)	A step for creating a mesh and initial condition for baroclinic channel test cases
initial_state.InitialState.setup()	Set up the test case in the work directory, including downloading any dependencies.
initial_state.InitialState.run()	Run this step of the test case

drying_slope

DryingSlope(mpas_core)	A test group for drying slope (wetting-and-drying) test cases
default.Default(test_group, resolution, ...)	The default drying_slope test case
default.Default.configure()	Modify the configuration options for this test case.
forward.Forward(test_case, resolution[, ...])	A step for performing forward MPAS-Ocean runs as part of drying slope test cases.
forward.Forward.run()	Run this step of the test case
initial_state.InitialState(test_case[, ...])	A step for creating a mesh and initial condition for drying slope test cases
initial_state.InitialState.run()	Run this step of the test case
viz.Viz(test_case[, damping_coeffs])	A step for visualizing drying slope results, as well as comparison with analytical solution and ROMS results.
viz.Viz.run()	Run this step of the test case

global_convergence

GlobalConvergence(mpas_core)

A test group for setting up global initial conditions and performing regression testing and dynamic adjustment for MPAS-Ocean

cosine_bell

CosineBell(test_group)	A test case for creating a global MPAS-Ocean mesh
CosineBell.configure()	Set config options for the test case
CosineBell.run()	Run each step of the testcase
mesh.Mesh(test_case, resolution)	A step for creating uniform global meshes
mesh.Mesh.run()	Run this step of the test case
mesh.Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
init.Init(test_case, resolution)	A step for an initial condition for for the cosine bell test case
init.Init.run()	Run this step of the testcase
forward.Forward(test_case, resolution)	A step for performing forward MPAS-Ocean runs as part of the cosine bell test case
forward.Forward.setup()	Set namelist options base on config options
forward.Forward.run()	Run this step of the testcase
forward.Forward.get_dt()	Get the time step
analysis.Analysis(test_case, resolutions)	A step for visualizing the output from the cosine bell test case
analysis.Analysis.run()	Run this step of the test case
analysis.Analysis.rmse(resolution)	Compute the RMSE for a given resolution

global_ocean

test cases and steps

GlobalOcean(mpas_core)	A test group for setting up global initial conditions and performing regression testing and dynamic adjustment for MPAS-Ocean
configure
analysis_test.AnalysisTest(test_group, mesh, ...)	A test case for performing a short forward run with an MPAS-Ocean global initial condition and check nearly all MPAS-Ocean analysis members to make sure they run successfully and output is identical to a baseline (if one is provided).
analysis_test.AnalysisTest.configure()	Modify the configuration options for this test case
analysis_test.AnalysisTest.run()	Run each step of the testcase
daily_output_test.DailyOutputTest(...)	A test case to test the output for the TimeSeriesStatMonthly analysis member in E3SM.
daily_output_test.DailyOutputTest.configure()	Modify the configuration options for this test case
daily_output_test.DailyOutputTest.run()	Run each step of the testcase
decomp_test.DecompTest(test_group, mesh, ...)	A test case for performing two short forward runs to make sure the results are identical with 4 and 8 cores
decomp_test.DecompTest.configure()	Modify the configuration options for this test case
decomp_test.DecompTest.run()	Run each step of the testcase
files_for_e3sm.FilesForE3SM(test_group, ...)	A test case for assembling files needed for MPAS-Ocean and MPAS-Seaice initial conditions in E3SM as well as files needed for diagnostics from the Meridional Overturning Circulation analysis member and MPAS-Analysis
files_for_e3sm.FilesForE3SM.configure()	Modify the configuration options for this test case
files_for_e3sm.FilesForE3SM.run()	Run each step of the test case.
files_for_e3sm.ocean_graph_partition.OceanGraphPartition(...)	A step for creating an E3SM ocean initial condition from the results of a dynamic-adjustment process to dissipate fast waves
files_for_e3sm.ocean_graph_partition.OceanGraphPartition.run()	Run this step of the testcase
files_for_e3sm.ocean_initial_condition.OceanInitialCondition(...)	A step for creating an E3SM ocean initial condition from the results of a dynamic-adjustment process to dissipate fast waves
files_for_e3sm.ocean_initial_condition.OceanInitialCondition.run()	Run this step of the testcase
files_for_e3sm.scrip.Scrip(test_case, ...)	A step for creating SCRIP files from the MPAS-Ocean mesh
files_for_e3sm.scrip.Scrip.run()	Run this step of the testcase
files_for_e3sm.seaice_initial_condition.SeaiceInitialCondition(...)	A step for creating an E3SM sea-ice initial condition from variables from an MPAS-Ocean restart file
files_for_e3sm.seaice_initial_condition.SeaiceInitialCondition.run()	Run this step of the testcase
files_for_e3sm.diagnostics_files.DiagnosticsFiles(...)	A step for creating files needed for the Meridional Overturning Circulation analysis member and diagnostics from MPAS-Analysis
files_for_e3sm.diagnostics_files.DiagnosticsFiles.run()	Run this step of the testcase
init.Init(test_group, mesh, ...)	A test case for creating initial conditions on a global MPAS-Ocean mesh
init.Init.configure()	Modify the configuration options for this test case
init.Init.run()	Run each step of the testcase
init.initial_state.InitialState(test_case, ...)	A step for creating a mesh and initial condition for baroclinic channel test cases
init.initial_state.InitialState.setup()	Set up the test case in the work directory, including downloading any dependencies.
init.initial_state.InitialState.run()	Run this step of the testcase
init.ssh_adjustment.SshAdjustment(test_case)	A step for iteratively adjusting the pressure from the weight of the ice shelf to match the sea-surface height as part of ice-shelf 2D test cases
init.ssh_adjustment.SshAdjustment.setup()	Set up the test case in the work directory, including downloading any dependencies
init.ssh_adjustment.SshAdjustment.run()	Run this step of the testcase
mesh.Mesh(test_group, mesh_name)	A test case for creating a global MPAS-Ocean mesh
mesh.Mesh.configure()	Modify the configuration options for this test case
mesh.Mesh.run()	Run each step of the testcase
mesh.cull.cull_mesh([with_cavities, ...])	First step of initializing the global ocean:
mesh.mesh.MeshStep(test_case, mesh_name, ...)	A step for creating a global MPAS-Ocean mesh
mesh.mesh.MeshStep.setup()	Set up the test case in the work directory, including downloading any dependencies.
mesh.mesh.MeshStep.run()	Run this step of the test case
mesh.mesh.MeshStep.build_cell_width_lat_lon()	A function for creating cell width array for this mesh on a regular latitude-longitude grid.
mesh.ec30to60.EC30to60Mesh(test_case, ...)	A step for creating EC30to60 and ECwISC30to60 meshes
mesh.ec30to60.EC30to60Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
mesh.ec30to60.dynamic_adjustment.EC30to60DynamicAdjustment(...)	A test case performing dynamic adjustment (dissipating fast-moving waves) from an initial condition on the EC30to60 MPAS-Ocean mesh
mesh.ec30to60.dynamic_adjustment.EC30to60DynamicAdjustment.configure()	Modify the configuration options for this test case
mesh.ec30to60.dynamic_adjustment.EC30to60DynamicAdjustment.run()	Run each step of the testcase
mesh.qu240.QU240Mesh(test_case, mesh_name, ...)	A step for creating QU240 and QUwISC240 meshes
mesh.qu240.QU240Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
mesh.qu240.dynamic_adjustment.QU240DynamicAdjustment(...)	A test case performing dynamic adjustment (dissipating fast-moving waves) from an initial condition on the QU240 MPAS-Ocean mesh
mesh.qu240.dynamic_adjustment.QU240DynamicAdjustment.configure()	Modify the configuration options for this test case
mesh.qu240.dynamic_adjustment.QU240DynamicAdjustment.run()	Run each step of the testcase
mesh.so12to60.SO12to60Mesh(test_case, ...)	A step for creating SOwISC12to60 meshes
mesh.so12to60.SO12to60Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
mesh.so12to60.dynamic_adjustment.SO12to60DynamicAdjustment(...)	A test case performing dynamic adjustment (dissipating fast-moving waves) from an initial condition on the SO12to60 MPAS-Ocean mesh
mesh.so12to60.dynamic_adjustment.SO12to60DynamicAdjustment.configure()	Modify the configuration options for this test case
mesh.so12to60.dynamic_adjustment.SO12to60DynamicAdjustment.run()	Run each step of the testcase
mesh.wc14.WC14Mesh(test_case, mesh_name, ...)	A step for creating SOwISC12to60 meshes
mesh.wc14.WC14Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
mesh.wc14.dynamic_adjustment.WC14DynamicAdjustment(...)	A test case performing dynamic adjustment (dissipating fast-moving waves) from an initial condition on the WC14 MPAS-Ocean mesh
mesh.wc14.dynamic_adjustment.WC14DynamicAdjustment.configure()	Modify the configuration options for this test case
mesh.wc14.dynamic_adjustment.WC14DynamicAdjustment.run()	Run each step of the testcase
performance_test.PerformanceTest(test_group, ...)	A test case for performing a short forward run with an MPAS-Ocean global initial condition assess performance and compare with previous results
performance_test.PerformanceTest.configure()	Modify the configuration options for this test case
performance_test.PerformanceTest.run()	Run each step of the testcase
restart_test.RestartTest(test_group, mesh, ...)	A test case for performing two forward run, one without a restart and one with to make sure the results are identical
restart_test.RestartTest.configure()	Modify the configuration options for this test case
restart_test.RestartTest.run()	Run each step of the testcase
threads_test.ThreadsTest(test_group, mesh, ...)	A test case for performing two short forward runs to make sure the results are identical with 1 and 2 thread per MPI process
threads_test.ThreadsTest.configure()	Modify the configuration options for this test case
threads_test.ThreadsTest.run()	Run each step of the testcase
dynamic_adjustment.DynamicAdjustment(...)	A parent test case for performing dynamic adjustment (dissipating fast-moving waves) from an MPAS-Ocean initial condition.
dynamic_adjustment.DynamicAdjustment.run()	Run each step of the testcase
forward.ForwardTestCase(test_group, mesh, ...)	A parent class for test cases for forward runs with global MPAS-Ocean mesh
forward.ForwardTestCase.configure()	Modify the configuration options for this test case
forward.ForwardTestCase.run()	Run each step of the testcase
forward.ForwardStep(test_case, mesh, init, ...)	A step for performing forward MPAS-Ocean runs as part of global ocean test cases.
forward.ForwardStep.setup()	Set up the test case in the work directory, including downloading any dependencies
forward.ForwardStep.run()	Run this step of the testcase

global_ocean framework

configure.configure_global_ocean(test_case, mesh)	Modify the configuration options for this test case
metadata.get_e3sm_mesh_names(config, levels)	Get short and long E3SM mesh name from config options and the given number of vertical levels (typically taken from an initial condition or restart file).
metadata.add_mesh_and_init_metadata(...)	Add MPAS mesh and initial condition metadata to NetCDF outputs of the given step

gotm

Gotm(mpas_core)

A test group for General Ocean Turbulence Model (GOTM) test cases

default

Default(test_group)	The default test case for the General Ocean Turbulence Model (GOTM) test group creates an initial condition on a 4 x 4 cell, doubly periodic grid, performs a short simulation, then vertical plots of the velocity and viscosity.
Default.validate()	Validate variables against a baseline
init.Init(test_case)	A step for creating a mesh and initial condition for General Ocean Turbulence Model (GOTM) test cases
init.Init.run()	Run this step of the test case
forward.Forward(test_case)	A step for performing forward MPAS-Ocean runs as part of General Ocean Turbulence Model (GOTM) test cases.
forward.Forward.run()	Run this step of the test case
analysis.Analysis(test_case)	A step for plotting the results of the default General Ocean Turbulence Model (GOTM) test case
analysis.Analysis.run()	Run this step of the test case

hurricane

test cases and steps

Hurricane(mpas_core)	A test group for hurricane simulations with MPAS-Ocean
configure
mesh.Mesh(test_group, mesh_name)	A test case for creating a global MPAS-Ocean mesh
mesh.Mesh.configure()	Modify the configuration options for this test case
mesh.Mesh.run()	Run each step of the testcase
mesh.dequ120at30cr10rr2.DEQU120at30cr10rr2Mesh(...)	A step for creating DEQU120at30cr10rr2 meshes
mesh.dequ120at30cr10rr2.DEQU120at30cr10rr2Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
init.Init(test_group, mesh, storm)	A test case for creating initial conditions on a global MPAS-Ocean mesh
init.Init.configure()	Modify the configuration options for this test case
init.Init.run()	Run each step of the testcase
init.create_pointstats_file.CreatePointstatsFile(...)	A step for creating the input file for the pointwiseStats analysis member
init.create_pointstats_file.CreatePointstatsFile.create_pointstats_file(...)	Find grid points nearest to observation stations and create pointwiseStats file
init.create_pointstats_file.CreatePointstatsFile.run()	Run this step of the testcase
init.initial_state.InitialState(test_case, mesh)	A step for creating a mesh and initial condition for hurricane test cases
init.initial_state.InitialState.setup()	Set up the test case in the work directory, including downloading any dependencies.
init.initial_state.InitialState.run()	Run this step of the testcase
init.interpolate_atm_forcing.InterpolateAtmForcing(...)	A step for interpolating the atmospheric wind velocities and pressure onto the MPAS-Ocean mesh to be used as time varying forcing in the forward run
init.interpolate_atm_forcing.InterpolateAtmForcing.interpolate_data_to_grid(...)	Interpolate time snaps of gridded data field to MPAS mesh
init.interpolate_atm_forcing.InterpolateAtmForcing.plot_interp_data(...)	Plot original gridded data and interpolated fields
init.interpolate_atm_forcing.InterpolateAtmForcing.write_to_file(...)	Write data to netCDF file
init.interpolate_atm_forcing.InterpolateAtmForcing.run()	Run this step of the test case
forward.Forward(test_group, mesh, storm, init)	A test case for performing a forward run for a hurricane case
forward.Forward.configure()	Modify the configuration options for this test case
forward.Forward.run()	Run each step of the testcase
forward.forward.ForwardStep(test_case, mesh, ...)	A step for performing forward MPAS-Ocean runs as part of hurricane test cases.
forward.forward.ForwardStep.setup()	Set up the test case in the work directory, including downloading any dependencies
forward.forward.ForwardStep.run()	Run this step of the testcase
analysis.Analysis(test_case, storm)	A step for producing ssh validation plots at observation stations
analysis.Analysis.setup()	Setup test case and download data
analysis.Analysis.read_pointstats(...)	Read the pointwiseStats data from the MPAS-Ocean run
analysis.Analysis.read_station_data(...)	Read the observed ssh timeseries data for a given station
analysis.Analysis.read_station_file(station_file)	Read file containing station locations and names
analysis.Analysis.run()	Run this step of the test case

ice_shelf_2d

IceShelf2d(mpas_core)	A test group for ice-shelf 2D test cases
configure(resolution, coord_type, config)	Modify the configuration options for this test case
default.Default(test_group, resolution, ...)	The default ice-shelf 2D test case, which performs a short forward run with the z-star vertical coordinate and with 15 iterations of adjustment to make the pressure from the weight of the ice shelf match the sea-surface height
default.Default.configure()	Modify the configuration options for this test case.
default.Default.run()	Run each step of the test case.
restart_test.RestartTest(test_group, ...)	A restart test case for the ice-shelf 2D test case test group, which makes sure the model produces identical results with one longer run and two shorter runs with a restart in between.
restart_test.RestartTest.configure()	Modify the configuration options for this test case.
restart_test.RestartTest.run()	Run each step of the test case.
forward.Forward(test_case, resolution[, ...])	A step for performing forward MPAS-Ocean runs as part of ice-shelf 2D test cases.
forward.Forward.setup()	Set up the test case in the work directory, including downloading any dependencies.
forward.Forward.run()	Run this step of the test case
initial_state.InitialState(test_case, resolution)	A step for creating a mesh and initial condition for ice-shelf 2D test cases
initial_state.InitialState.run()	Run this step of the test case
ssh_adjustment.SshAdjustment(test_case[, ...])	A step for iteratively adjusting the pressure from the weight of the ice shelf to match the sea-surface height as part of ice-shelf 2D test cases
ssh_adjustment.SshAdjustment.setup()	Set up the test case in the work directory, including downloading any dependencies.
ssh_adjustment.SshAdjustment.run()	Run this step of the test case
viz.Viz(test_case)	A step for visualizing a cross-section through the 2D ice-shelf domain
viz.Viz.run()	Run this step of the test case

internal_wave

InternalWave(mpas_core)	A test group for General Ocean Turbulence Model (GOTM) test cases
default.Default(test_group)	The default test case for the internal wave test
default.Default.validate()	Validate variables against a baseline
rpe_test.RpeTest(test_group)	The reference potential energy (RPE) test case for the internal wave test group performs a 20-day integration of the model forward in time at 5 different values of the viscosity at the given resolution.
rpe_test.analysis.Analysis(test_case, nus)	A step for plotting the results of a series of RPE runs in the internal wave test group
rpe_test.analysis.Analysis.run()	Run this step of the test case
ten_day_test.TenDayTest(test_group)	The default test case for the internal wave test
ten_day_test.TenDayTest.validate()	Validate variables against a baseline
forward.Forward(test_case[, name, subdir, ...])	A step for performing forward MPAS-Ocean runs as part of internal wave test cases.
forward.Forward.run()	Run this step of the test case
initial_state.InitialState(test_case)	A step for creating a mesh and initial condition for internal wave test cases
initial_state.InitialState.run()	Run this step of the test case
viz.Viz(test_case)	A step for visualizing a cross-section through the internal wave
viz.Viz.run()	Run this step of the test case

isomip_plus

IsomipPlus(mpas_core)	A test group for ice-shelf 2D test cases
ocean_test.OceanTest(test_group, resolution, ...)	An ISOMIP+ test case
ocean_test.OceanTest.configure()	Modify the configuration options for this test case.
ocean_test.OceanTest.run()	Run each step of the test case
viz.Viz(test_case, resolution, experiment)	A step for visualizing output from an ISOMIP+ simulation
viz.Viz.run()	Run this step of the test case
viz.file_complete(ds, fileName)	Find out if the file already has the same number of time slices as the monthly-mean data set
viz.plot.TimeSeriesPlotter([inFolder, ...])	A plotter object to hold on to some info needed for plotting time series from ISOMIP+ simulation results
viz.plot.TimeSeriesPlotter.plot_melt_time_series([...])	Plot a series of image for each of several variables related to melt at the ice shelf-ocean interface: mean melt rate, total melt flux, mean thermal driving, mean friction velocity
viz.plot.TimeSeriesPlotter.plot_time_series(da, ...)
viz.plot.MoviePlotter(inFolder, ...)	A plotter object to hold on to some info needed for plotting images from ISOMIP+ simulation results
viz.plot.MoviePlotter.plot_barotropic_streamfunction([...])	Plot a series of image of the barotropic streamfunction
viz.plot.MoviePlotter.plot_overturning_streamfunction([...])	Plot a series of image of the overturning streamfunction
viz.plot.MoviePlotter.plot_melt_rates([...])	Plot a series of image of the melt rate
viz.plot.MoviePlotter.plot_ice_shelf_boundary_variables()	Plot a series of image for each of several variables related to the ice shelf-ocean interface: heat flux from the ocean, heat flux into the ice, thermal driving, haline driving, and the friction velocity under ice
viz.plot.MoviePlotter.plot_temperature()	Plot a series of images of temperature at the sea surface or ice-ocean interface, sea floor and in an x-z section
viz.plot.MoviePlotter.plot_salinity()	Plot a series of images of salinity at the sea surface or ice-ocean interface, sea floor and in an x-z section
viz.plot.MoviePlotter.plot_potential_density()	Plot a series of images of salinity at the sea surface or ice-ocean interface, sea floor and in an x-z section
viz.plot.MoviePlotter.plot_horiz_series(da, ...)	Plot a series of image of a given variable
viz.plot.MoviePlotter.plot_3d_field_top_bot_section(da, ...)	Plot a series of images of a given 3D variable showing the value at the top (sea surface or ice-ocean interface), sea floor and in an x-z section
viz.plot.MoviePlotter.plot_layer_interfaces([...])	Plot layer interfaces, the sea surface height and the bottom topography of the cross section at fixed y.
viz.plot.MoviePlotter.images_to_movies(outFolder)	Convert all the image sequences into movies with ffmpeg
evap.update_evaporation_flux(...)	Update the "evaporation" fluxes used to keep sea level under control for the ISOMIP+ experiments.
forward.Forward(test_case, resolution, ...)	A step for performing forward MPAS-Ocean runs as part of ice-shelf 2D test cases.
forward.Forward.setup()	Set up the test case in the work directory, including downloading any dependencies.
forward.Forward.run()	Run this step of the test case
geom.process_input_geometry(inFileName, ...)	Process the BISICLES input geometry from ISOMIP+.
geom.interpolate_ocean_mask(dsMesh, dsGeom, ...)	Interpolate the ocean mask from the original BISICLES grid to the MPAS mesh.
initial_state.InitialState(test_case, ...)	A step for creating a mesh and initial condition for ISOMIP+ test cases
initial_state.InitialState.run()	Run this step of the test case
misomip.Misomip(test_case, resolution, ...)	A step for interpolating output to the MISOMIP1 grid from an ISOMIP+ simulation
misomip.Misomip.run()	Run this step of the test case
ssh_adjustment.SshAdjustment(test_case, ...)	A step for iteratively adjusting the pressure from the weight of the ice shelf to match the sea-surface height as part of ice-shelf 2D test cases
ssh_adjustment.SshAdjustment.setup()	Set up the test case in the work directory, including downloading any dependencies.
ssh_adjustment.SshAdjustment.run()	Run this step of the test case
streamfunction.Streamfunction(test_case, ...)	A step for computing the barotropic and overturning streamfunctions from ISOMIP+ simulation results
streamfunction.Streamfunction.run()	Run this step of the test case

planar_convergence

PlanarConvergence(mpas_core)	A test group for testing horizontal advection in MPAS-Ocean
conv_init.ConvInit(test_case, resolution)	A step for creating a mesh for a given resolution in a planar convergence test case.
conv_init.ConvInit.run()	Run this step of the test case
conv_test_case.ConvTestCase(test_group, name)	A test case for various convergence tests on in MPAS-Ocean with planar, doubly periodic meshes
conv_test_case.ConvTestCase.configure()	Set config options for the test case
conv_test_case.ConvTestCase.run()	Run each step of the testcase
conv_test_case.ConvTestCase.update_cores()	Update the number of cores and min_cores for each forward step
forward.Forward(test_case, resolution)	A step for performing forward MPAS-Ocean runs as part of a planar convergence test case
forward.Forward.setup()	Set namelist options base on config options
forward.Forward.run()	Run this step of the testcase
forward.Forward.get_dt_duration()	Get the time step and run duration as namelist options from config options

horizontal_advection

HorizontalAdvection(test_group)	A test case for testing horizontal advection in MPAS-Ocean with planar, doubly periodic meshes
HorizontalAdvection.configure()	Set config options for the test case
HorizontalAdvection.run()	Run each step of the testcase
init.Init(test_case, resolution)	A step for creating an initial_condition for advection convergence test case
init.Init.run()	Run this step of the test case
analysis.Analysis(test_case, resolutions)	A step for visualizing the output from the advection convergence test case
analysis.Analysis.run()	Run this step of the test case
analysis.Analysis.rmse(resolution, variable)	Compute the RMSE for a given resolution

soma

Soma(mpas_core)	A test group for Simulating Ocean Mesoscale Activity (SOMA) test cases
soma_test_case.SomaTestCase(test_group, ...)	The class for all test cases in the SOMA test group.
soma_test_case.SomaTestCase.validate()	Test cases can override this method to perform validation of variables
analysis.Analysis(test_case, resolution)	A step for verifying that temperature and salinity profiles for SOMA case from particle interpolations are consistent with initialized profiles
analysis.Analysis.run()	Run this step of the test case
forward.Forward(test_case, resolution, ...)	A step for performing forward MPAS-Ocean runs as part of SOMA test cases.
forward.Forward.run()	Run this step of the test case
initial_state.InitialState(test_case, ...)	A step for creating a mesh and initial condition for SOMA test cases
initial_state.InitialState.run()	Run this step of the test case

sphere_transport

SphereTransport(mpas_core)

A test group for testing algorithms for passive tracer advection on the sphere

correlated_tracers_2d

CorrelatedTracers2D(test_group)	A test case for 2D transport on the sphere
CorrelatedTracers2D.configure()	Set config options for the test case
CorrelatedTracers2D.run()	Run each step of the testcase
mesh.Mesh(test_case, resolution)	A step for creating uniform global meshes
mesh.Mesh.run()	Run this step of the test case
mesh.Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
init.Init(test_case, resolution)	A step for an initial condition for for the cosine bell test case
init.Init.run()	Run this step of the testcase
forward.Forward(test_case, resolution, ...)	A step for performing forward MPAS-Ocean runs as part of the
forward.Forward.setup()	Set namelist options base on config options
forward.Forward.run()	Run this step of the testcase
forward.Forward.get_timestep_str()	These tests expect the time step to be input in units of minutes, but MPAS requires an "HH:MM:SS" string.
analysis.Analysis(test_case, resolutions)	A step for visualizing the output from the correlatedTracers2D test case
analysis.Analysis.run()	Run this step of the test case

divergent_2d

Divergent2D(test_group)	A test case for 2D transport on the sphere
Divergent2D.configure()	Set config options for the test case
Divergent2D.run()	Run each step of the testcase
mesh.Mesh(test_case, resolution)	A step for creating uniform global meshes
mesh.Mesh.run()	Run this step of the test case
mesh.Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
init.Init(test_case, resolution)	A step for an initial condition for for the cosine bell test case
init.Init.run()	Run this step of the testcase
forward.Forward(test_case, resolution, ...)	A step for performing forward MPAS-Ocean runs as part of the divergent_2d
forward.Forward.setup()	Set namelist options base on config options
forward.Forward.run()	Run this step of the testcase
forward.Forward.get_timestep_str()	These tests expect the time step to be input in units of minutes, but MPAS requires an "HH:MM:SS" string.
analysis.Analysis(test_case, resolutions)	A step for visualizing the output from the divergent2D test case
analysis.Analysis.run()	Run this step of the test case

nondivergent_2d

Nondivergent2D(test_group)	A test case for 2D transport on the sphere
Nondivergent2D.configure()	Set config options for the test case
Nondivergent2D.run()	Run each step of the testcase
mesh.Mesh(test_case, resolution)	A step for creating uniform global meshes
mesh.Mesh.run()	Run this step of the test case
mesh.Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
init.Init(test_case, resolution)	A step for an initial condition for for the cosine bell test case
init.Init.run()	Run this step of the testcase
forward.Forward(test_case, resolution, ...)	A step for performing forward MPAS-Ocean runs as part of the
forward.Forward.setup()	Set namelist options base on config options
forward.Forward.run()	Run this step of the testcase
forward.Forward.get_timestep_str()	These tests expect the time step to be input in units of minutes, but MPAS requires an "HH:MM:SS" string.
analysis.Analysis(test_case, resolutions)	A step for visualizing the output from the nondivergent2D test case
analysis.Analysis.run()	Run this step of the test case

rotation_2d

Rotation2D(test_group)	A test case for 2D transport on the sphere
Rotation2D.configure()	Set config options for the test case
Rotation2D.run()	Run each step of the testcase
mesh.Mesh(test_case, resolution)	A step for creating uniform global meshes
mesh.Mesh.run()	Run this step of the test case
mesh.Mesh.build_cell_width_lat_lon()	Create cell width array for this mesh on a regular latitude-longitude grid
init.Init(test_case, resolution)	A step for an initial condition for for the cosine bell test case
init.Init.run()	Run this step of the testcase
forward.Forward(test_case, resolution, ...)	A step for performing forward MPAS-Ocean runs as part of the rotation_2d
forward.Forward.setup()	Set namelist options base on config options
forward.Forward.run()	Run this step of the testcase
forward.Forward.get_timestep_str()	These tests expect the time step to be input in units of minutes,
analysis.Analysis(test_case, resolutions)	A step for visualizing the output from the rotation_2d test case
analysis.Analysis.run()	Run this step of the test case

sphere_transport framework

process_output.compute_error_from_output_ncfile(dataset)	Given a netCDF4 Dataset associated with the output.nc file from a test case in the sphere_transport test group, this function computes the linf and l2 relative error values by comparing the final time step to the initial condition.
process_output.compute_convergence_rates(...)	Given a set of approximate mesh sizes (dlambda) and the corresponding linf and l2 relative error values, this function computes the approximate convergence rates for each error.
process_output.print_error_conv_table(...)	Print error values and approximate convergence rates to the console as a table.
process_output.read_ncl_rgb_file(cmap_filename)	Read a .rgb file from the NCAR Command Language, and return a matplotlib colormap.
process_output.plot_sol(fig, tcname, dataset)	Plot the solution at time 0, t = T/2, and T=T for test cases in the sphere_transport test group.
process_output.make_convergence_arrays(tcdata)	Collects data from a set of test case runs at different resolutions to use for convergence data analysis and plotting.
process_output.print_data_as_csv(tcname, tcdata)	Print test case data in csv format
process_output.plot_convergence(ax, tcname, ...)	Creates a convergence plot for a test case from the sphere_transport test group.
process_output.plot_filament(ax, tcname, ...)	Plot the "filament norm," as in figure 5 of LSPT2012.
process_output.plot_over_and_undershoot_errors(ax, ...)	Plots over- and under-shoot error as a function of time.

ziso

Ziso(mpas_core)	A test group for Zonally Invariant Southern Ocean (ZISO) test cases
configure(name, resolution, config)	Modify the configuration options for this test case
ZisoTestCase(test_group, resolution, ...)	The default test case for the ZISO test group simply creates the mesh and initial condition, then performs a short forward run with analysis members but without frazil.
ZisoTestCase.configure()	Modify the configuration options for this test case.
ZisoTestCase.run()	Run each step of the test case.
with_frazil.WithFrazil(test_group, resolution)	The with frazil test case for the ZISO test group simply creates the mesh and initial condition, then performs a short forward run including frazil formation.
with_frazil.WithFrazil.configure()	Modify the configuration options for this test case.
with_frazil.WithFrazil.run()	Run each step of the test case.
forward.Forward(test_case, resolution[, ...])	A step for performing forward MPAS-Ocean runs as part of ZISO test cases.
forward.Forward.setup()	Set up the test case in the work directory, including downloading any dependencies.
forward.Forward.run()	Run this step of the test case
initial_state.InitialState(test_case, ...)	A step for creating a mesh and initial condition for ZISO test cases
initial_state.InitialState.run()	Run this step of the test case

ocean framework

haney.compute_haney_number(ds_mesh, ...[, ...])	Compute the Haney number rx1 for each edge, and interpolate it to cells
iceshelf.compute_land_ice_pressure_and_draft(...)	Compute the pressure from and overlying ice shelf and the ice-shelf draft
iceshelf.adjust_ssh(variable, ...)	Adjust the sea surface height or land-ice pressure to be dynamically consistent with one another.
particles.write(init_filename, ...[, types, ...])	Write an initial condition for particles partitioned across cores
particles.remap_particles(init_filename, ...)	Remap particles onto a new grid decomposition.
plot.plot_initial_state([input_file_name, ...])	creates histogram plots of the initial condition
plot.plot_vertical_grid(grid_filename, config)	Plot the vertical grid
vertical.init_vertical_coord(config, ds)	Create a vertical coordinate based on the config options in the vertical_grid section and the bottomDepth and ssh variables of the mesh data set.
vertical.grid_1d.generate_1d_grid(config)	Generate a vertical grid for a test case, using the config options in the vertical_grid section
vertical.grid_1d.write_1d_grid(interfaces, ...)	write the vertical grid to a file
vertical.partial_cells.alter_bottom_depth(...)	Alter bottomDepth and maxLevelCell for full or partial top cells, if requested
vertical.partial_cells.alter_ssh(config, ...)	Alter ssh and maxLevelCell for full or partial top cells, if requested
vertical.zlevel.init_z_level_vertical_coord(...)	Create a z-level vertical coordinate based on the config options in the vertical_grid section and the bottomDepth and ssh variables of the mesh data set.
vertical.zlevel.compute_min_max_level_cell(...)	Compute minLevelCell and maxLevelCell indices as well as a cell mask for the given reference grid and top and bottom topography.
vertical.zlevel.compute_z_level_layer_thickness(...)	Compute z-level layer thickness from ssh and bottomDepth
vertical.zlevel.compute_z_level_resting_thickness(...)	Compute z-level resting thickness by "unstretching" layerThickness based on ssh and bottomDepth
vertical.zstar.init_z_star_vertical_coord(...)	Create a z-star vertical coordinate based on the config options in the vertical_grid section and the bottomDepth and ssh variables of the mesh data set.