Model outputs and visualization

VTK outputs

By default Thetis stores outputs in VTK format, suitable for visualization with ParaView.

By default results are stored to outputs sub-directory. Users can define a custom output directory with ModelOptions3d.output_directory option. The fields to be exported are defined with ModelOptions3d.fields_to_export list.

For example to store only 2D water elevation and 3D temperature fields to mydir directory one would set:

solver_obj = FlowSolver(...)
options = solver_obj.options
options.outputdir = 'mydir'
options.fields_to_export = ['elev_2d', 'temp_3d']

For a full list of available fields, and their *.pvd file names, refer to physical fields page. Note that fields are exported only if they are defined; e.g. exporting a field 'temp_3d' is ignored if you are running a 2D model.

In some cases it is useful to suppress all output to disk (e.g. with some test cases). This can be achieved by setting ModelOptions3d.no_exports option to True.

See Firedrake’s documentation for more information on visualization cababilities.

Visualizing stored ParaView state files

Creating a complex visualization is a time consuming task. ParaView allows users to store the active visualization state into a file (File → Save State), and restore it later (File → Load State).

To quickly launch a previously saved visualization you can use the visualize_output.py utility. This script opens a ParaView state file using model outputs in any user-defined directory:

visualize_output.py <outputdir> <statefile.pvsm>

The script replaces all *.pvd file paths in statefile.pvsm to point to outputdir, and launches ParaView. You’ll need to have paraview in your seach path for this to work. Run visualize-output.py -h to see full usage instructions.

Note

If you add ParaView’s bin directory to your PATH environment variable, be careful: ParaView has its own python and mpiexec binaries which may break your Firedrake installation. It’s advisable to modify PATH before activating the Firedrake virtual environment, or appending (rather than prepending) the directory to PATH.

HDF5 outputs

Thetis also stores model state variables in lossless HDF5 format that allows loading a previous model state from disk.

Note

Currently HDF5 checkpointing file can only be loaded on same number of MPI processes as were used to create the file. See Firedrake’s documentation for more information.

The fields to be exported in HDF5 format are defined in ModelOptions3d.fields_to_export_hdf5 list, that is empty by default. The files are stored in outputdir/hdf5 directory in format Elevation2d_00001.h5 where the prefix is the output file name of the field, followed by the export index. HDF5 files are stored at the same time intervals as VTK files, defined by ModelOptions3d.simulation_export_time option.

In order to be able to restart a previous simulation, one has to export all the prognostic variables that define the model state. For a 2D simulation this implies:

options.fields_to_export_hdf5 = ['elev_2d', 'uv_2d']

while a 3D simulation requires:

options.fields_to_export_hdf5 = ['elev_2d', 'uv_2d', 'uv_3d',
                                 'salt_3d', 'temp_3d', 'tke_3d', 'psi_3d']

Restarting a simulation

If you have stored the required HDF5 files, you can continue a simulation using load_state() method, provided that you use the same mesh and the same number of MPI processes. This call replaces the assign_initial_conditions() call. If initial conditions are not set, add load_state call above the iterate() call.

In the simplest form, one only defines the export index that is used as initial condition:

solver_obj.load_state(155)

This also loads simulation time from the stored state. It is also possible to load the initial state from another (sub-) directory:

solver_obj.load_state(155, outputdir='other_outputdir')