Hi, I am CPlantBox

For simulations in https://doi.org/10.1101/810507 please use branch isp

I can :

1. Create multiple plant structure
2. Coupling with PiafMunch, and make carbon and water flow inside of the plant.

Try me 1 click

The most convenient way is to use google colab, which is a Linux virtual machine with jupyter notebook interface. You can click the link to follow the guide there, just to click some buttons and you will be able to create plants here is the link to use it.

build local

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

Linux

If you have and, you can set up CPlantBox (with or without the dumux-rosi extension) via an install script.
This installation method requires ubuntu >= 20.04 and python >= 3.7.
For CPlantBox without the dumux-rosi extension, download the python file "installCPlantBox.py".
Run

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 with the dumux-rosi extension, download the python file "installDumuxRosi_Ubuntu.py" (based on the dumux installation file).
run

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. 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