Root-CyNAPS : Root Cycling Nitrogen Across Plant Scales

An architectured FSPM root model to simulate nitrogen acquisition and rhizodeposition

Overview

This module aims at simulating explicit processes of root nitrogen uptake and rhizodeposition by aggregating a segment-scale nutrient balance model over the root system architecture.

TODO

Installation option 1 : stable installation with docker (about 6Gb)

1. First, download the docker engine : https://docs.docker.com/engine/install/

2. Then create a project directory (example : PythonProjects), and clone this repository from command line :

cd .../PythonProjects
git clone https://forgemia.inra.fr/tristan.gerault/root_cynaps.git

3. Finally, build the docker image with the following command

cd root_cynaps
docker image build -t root_cynaps .
docker run root_cynaps

(For developpers, build this image directly into your IDE)'

Installation option 2 : more classic but unstable installation with conda + mamba (about 4Gb)

First, clone the repository :

git clone https://forgemia.inra.fr/tristan.gerault/root_cynaps.git

Intall the lastest version of conda : https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html

Then, install necessary packages with the following requirements files. cd to the root_cynaps directory, then :

• On Windows :

requirements.bat

• On Linux :

bash requirements.sh

• On MacOs : No available yet

Running example code

cd to the simulations/running_example folder, then run :

python main.py