Data I/O

Executing DORiE requires several input files, some of which are optional and depending on the mode the program runs in. The configuration input files can typically be created and manipulated by any text editor. For larger portions of input data we use HDF5, a hierachical binary data format. These files can easily be written using the h5py Python module.

DORiE writes output files in the VTK format, a filetype suitable for storing grid-based datasets. These files can be evaluated interactively using Paraview. The VTK software library can be included into C++ code and even has Python bindings.

Input Files

Templates for the required files can conveniently be generated with the CLI.

Type

Format

Description

Templates

Configuration File

.ini

The main input file for the solver.

config.ini

Parameterization Data File

.yml

Specifies the soil and solute parameterization type(s) and parameters.

richards_param.yml, transport_param.yml

Boundary Condition Data File

.yml

Specifies the boundary segmentation and the boundary conditions.

richards_bc.yml, transport_bc.yml

GMSH Mesh File (optional)

.gmsh

Mesh with possibly complicated geometry to build an unstructured grid from.

Grid Mapping H5 File (optional)

.h5

Used to generate heterogeneous soil architectures and boundary segmentations for rectangular grids.

Scaling Field H5 Files (optional)

.h5

Datasets for interpolating local heterogeneities in the parameterization.

Output Files

  • Time Stamp File (.pvd): Lists the time step information and the respective VTK output files of a single program run. This file is always saved into the directory from which DORiE was executed.

  • VTK Files (.vtu): The output data in unstructured grid format. It contains multiple multiple datasets depending on the type of model:

    Richards
    • head: Matric head \(h_m \, [\mathrm{m}]\)

    • K0: Saturated conductivity \(K_0 \, [\mathrm{ms}^{-1}]\)

    • flux: Water flux \(\mathbf{j}_w \, [\mathrm{ms}^{-1}]\) (not reconstructed!)

    • flux_RT<k-1>: Reconstructed water flux \(\mathbf{j}_{w, \mathrm{rc}} \, [\mathrm{ms}^{-1}]\) (if enabled!)

    • theta_w: Volumetric water content \(\theta \, [\mathrm{-}]\)

    • Theta: Water saturation \(\Theta \, [\mathrm{-}]\)

    Transport
    • solute: Solute concentration in water phase \(c_w \, [\mathrm{kg}\mathrm{m}^{-3}]\)

    • solute_total: Total solute concentration \(c_t \, [\mathrm{kg}\mathrm{m}^{-3}]\)

    • micro_peclet: Microscopic peclet number \(\mathsf{pe_\mu} \, [-]\)

    • flux_RT<k-1>: Reconstructed solute flux \(\mathbf{j}_{s, \mathrm{rc}} \, [\mathrm{kg}\,\mathrm{m}^{-2}\mathrm{s}^{-1}]\) (if enabled!)

    • eff_hd_dispersion: Hydrodynamic dispersion tensor \(\mathsf{D}_\mathsf{hd} \, [\mathrm{m}^2\mathrm{s}^{-1}]\) (if enabled!)

  • VTK Parallel Collection Files (.pvtu): Merging multiple VTK files in case DORiE is run in parallel.