File tree

When running the code, the following tree is created:

/data_name
├── /HDF5
│   ├── /meshes
│   ├── data.h5
│   ├── data_timestamp.dat
│   ├── subdomains.pvd, *.pvtu, *.vtu
│   └── mesh.h5, mesh.xdmf
├── /anim
├── /img
├── /paraview
│   ├── /initial_condition
│   ├── *.h5, *.xdmf
├── /source_code
├── /tracers
├── empty_cells.dat
├── picard_iter.dat
└── statistics.dat

Below, the data in individual directories are described.

/HDF5

  • The directory meshes contains files named mesh_*.h5, which is an HDF5 file containing the mesh for each time output. These files can be used for plotting through matplotlib and cannot be opened in Paraview.

  • The file data.h5 contains functions defined in Paraview_Output parameter, but always at least those that are needed for restarting the computation. Data from this file are used for plotting and reloading the simulation.

  • The file data_timestamp.dat contains information about the steps when the data were written (time, simulation step, position in HDF5 file)

  • Files starting subdomains* contain Paraview-readable format of the subdomains, which enables to check whether the boundaries were defined and recognized correctly.

  • Files mesh.h5 and mesh.xdmf contain mesh in paraview-readable format.


/anim and /img

These are auxiliary directories that can be used in case of plotting images and making animations from the results.


/paraview

  • Contains pairs of *.xdmf and *.h5 for each of the physical quantities specified in Paraview_Output (again at least those that are needed for restarting the computation).

  • The directory initial_condition contains quantities that were used as an initial condition and specified in Paraview_Output_Ini


/source_code

Contains all parts of the source code needed for reproduction of the results.

/tracers

Contains files with tracer properties for each step of output specified in Tracers_Output.