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Folder structure

DanielLeitner edited this page Nov 27, 2020 · 11 revisions

The new upcoming folder structure...

cpp/

Python binding code and examples in C++

  • python_binding/

    the C++ part of the dumux-rosi Python binding (Python part is in python/modules/)

  • roots_1p/

    water movement in root systems (no soil)

  • roots_1pnc/

    water and solute movement in root systems (no soil)

  • soil_richards/

    water movement in soil (no root system)

  • soil_richardsnc/

    water and solute movement in soil (no root system)

  • soil_tracer/

    solute movement under a given flow field (no root system)

  • coupled_1p_richards/

    water movement in root-soil system (uses roots_1p/ and soil_richards/)

  • coupled_1pnc_richards/

    water movement in root-soil system, additionally solute or hormone movement within the roots (uses roots_1pnc/ and soil_richards/)

  • coupled_1pnc_richardsnc/

    water and solute movement in root-soil system (uses roots_1pnc/ and soil_richardsnc/)

  • modelparameter/

    CPlantBox parameters, that are used in the examples (in the old deprecated format), the new xml format is located in CPlantBox/modelparameter

The sub-folders of the examples:

  • python/

    scripts to run and post process the examples

  • input/

    the DuMux input files

  • grids/

    numerical grids (dgf, vtp, vtu, ...) used in the examples

python/

Examples that are using the dumux-rosi Python binding. They are organized in three sub folders regarding their simulation domain (soil, roots, or coupled):

  • soil/

    bulk soil only (e.g. water and or solute transport)

  • roots/

    root system only (e.g. water or hormone movement within the xylem)

  • coupled/

    root soil interaction models

Additional folders for common resources:

  • modules/

    Contains the Python parts of the pybind11 DuMux bindings and simple Python finite volume solvers. Auxiliary tools that are are also useful for CPlantBox (e.g. working with vtk, rsml, or the Python part of the XylemFlux class) are locaed in CPlantBox/src/python_modules.

applications/

Applications and auxiliary scripts

  • suf/

    scripts for calculating the surface uptake fraction, and equivalent soil potential

  • grid_generation/

    scripts for grid generation (TODO) not quite sure what is in there

grids/

Numerical grids (vtp, dgf, msh, ...)

doc/

Contains documentation

dumux/

Modifications and additions to DuMux as used in dumux-rosi (usually do not touch)

test/

Will contain python scripts that (unit tests and integration tests)

scripts/

Contains small scripts (e.g. shell scripts, paraview scripts, ...)

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