MECHA is an explicit cross-section model of the root hydraulic anatomy which connects hydraulic concepts across scales.
The model computes horizontal water flow at the level of individual cells, quantifies the contribution of water composite pathways, and predicts root radial permeability (kr), using detailed anatomical descriptions and experimental data on the permeability of cell walls (kw), membranes (Lp) and the conductance of individual plasmodesmata (KPD).
MECHA was coded in Python, and is therefore platform independant. It can be run on Windows, Linux and MacOS
The source code of MECHA is available on github: https://github.com/MECHARoot/MECHA
The github repo also contain example parameter files needed to run MECHA. You do not need your own data to try it out.
The first step before running MECH is to install a working version for Python. Installation of Python are available here: https://www.python.org/downloads/
MECHA is built upon a handfull of external libraries. You will need to install them before using the model.
These libraries can be install using pip. In the Terminal or Console, enter:
pip install numpy pip install scipy pip install networkx==1.9.1 pip install lxml pip install matplotlib
In the Terminal or Console enter the following lines:
cd "$PATH_TO_FOLDER_CONTAINING_MECHA" python mecha_all.py
Feeling adventurous? Check out the source code.View source code
MECHA uses four parameters files as input, stored in the
/in folder in the main MECHA directory:
General.xml: General simulation parameters
BC.xml: Boundary conditions for the simulation. This is where you choose wether the soil is dry, wet, or only partially touch the root.
Geometry.xml: Parameters for the root section geometry. This is where you define which root section to use in the simulation.
Hydraulics.xml: Hydraulic parameters of the different variables in the simulation
MECHA output files in a folder defined in the
General.xml input file, under the
Output tag. Different type of files are generated:
*.PVTK files: These are geometry files that can be open in Paraview
Macro_prop_i.txt files: Theses files contain synthetic informations about the simulation results. They contain the radial data.
MECHA what first used here:
Going with the flow. Multiscale insights into the composite nature of water transport in roots Valentin Couvreur, Marc Faget, Guillaume Lobet, Mathieu Javaux, François Chaumont and Xavier Draye
Plant Physiology, 2018