Awesome

Hi, I am CPlantBox

I can :

Create multiple plant structures
Simulate the carbon transport (coupling with PiafMunch) and water flow inside of the plant
Simulate the solute transport and water flow in the soil (coupling with DuMux)

Try me 1 click

You can discover CPlantBox with this web-based application designed for conduct and visualize plant growth simulations. It is part of Xiaoran Zhou's PhD thesis. the source code is avialable at <a href="https://github.com/xiaoranzhou/cpb">github-xiaoranzhou

Cloud-based notebooks are also available:

build local

semi-automated CPlantBox (with dumux-rosi) installation via python script (recommended)

Linux

This installation method requires ubuntu >= 20.04 and python >= 3.7.
For CPlantBox <ins>without</ins> the dumux-rosi extension, download the python file "installCPlantBox.py".
Run

sudo apt-get update
sudo apt-get upgrade
[ ! -d 'cpbenv' ] && python3 -m venv cpbenv &&  source cpbenv/bin/activate ||  source cpbenv/bin/activate
wget https://raw.githubusercontent.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/master/installCPlantBox.py
python3 installCPlantBox.py

It will create a "CPB" folder and install inside the dependencies necessary to run CPlantBox.
For CPlantBox <ins>with</ins> the dumux-rosi extension, download the python file "installDumuxRosi_Ubuntu.py" (based on the dumux installation file).
run

sudo apt-get update
sudo apt-get upgrade
[ ! -d 'cpbenv' ] && python3 -m venv cpbenv &&  source cpbenv/bin/activate ||  source cpbenv/bin/activate
wget https://raw.githubusercontent.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/master/installDumuxRosi_Ubuntu.py
python3 installDumuxRosi_Ubuntu.py

This will create a "DUMUX" folder and install inside the dependencies necessary to run dumux-rosi. CPlantBox is setup within the virtual environment 'cpbenv'.
Do not forget to reactivate the 'cpbenv' environment when using CPlantBox:

source cpbenv/bin/activate

This script might work on other linux OS but has not been tested.

windows

CPlantBox is currently not available on windows. Some pointers to setup a linux environment on windows are given on the wiki.

manual linux installation

Clone the repository by running:

git clone --depth 1 -b master https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox.git

Run CMake which configures the CPlantBox libraries by

cmake . && make

in the root folder, and run some Python tutorial examples (see tutorial/latex/PlantBox_RootSytem), e.g

cd tutorial/examples/python
python3 example1a.py

The dependecies are listed in the requirements.txt file.

Installation on the JSC agrocluster

Refer to the wiki:
https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/wiki/CPlantBox-on-the-J%C3%BClich-Supercomputer-cluster

Folder sructure

/modelparameter Plant parameter files
/src CPlantBox C++ codes
/test Python tests for all CPlantBox classes
/tutorial learn to use CPlantBox
/experimental Specific applications (in sub-folders). contrary to scripts in /tutorial, might not be kept up to date

Code documentation

Create the documentation by running doxygen in the folder $ doxygen doxy_config

The documentation will be located in the folder /doc. Compile doc/latex/refman.tex to generate the full doxygen documentation in doc/latex/refman.pdf.

Collaboration diagrams give an overview of the code in folder /docs.

Examples

Simulation videos availabe in Youtube Channel https://www.youtube.com/channel/UCPK-pFfpK94jiamgwHxX32Q