DFMFON, stands for Delft3D-Flexible Mesh (DFM) and MesoFON (MFON) is an open-source software written in Python to mechanistically simulate the Mangrove and Hydromorphology development. We achieve that by coupling multi-paradigm of individual-based mangrove model MFON and process-based hydromorphodynamic model DFM.
This model is developed as part of the PhD research by Sebrian Beselly at IHE Delft and Delft University of Technology.
Publication describing the DFMFON
Modelling mangrove-mudflat dynamics with a coupled individual-based-hydro-morphodynamic model (open access)
As climate-change-driven extremes potentially make coastal areas more vulnerable, mangroves can help sustainably protect the coasts. There is a substantial understanding of both mangrove dynamics and hydro-morphodynamic processes. However, the knowledge of complex eco-geomorphic interactions with physical-environmental stressors remains lacking. We introduce a novel coupled modelling approach consisting of an individual-based mangrove (mesoFON) and a process-based hydromorphodynamic model (Delft3D-FM). This coupled model is unique because it resolves spatiotemporal processes, including tidal, seasonal, and decadal environmental changes (water level, flow, sediment availability, and salinity) with full life-stages (propagule, seedling, sapling, mature) mangrove interaction. It allows us to mechanistically simulate forest expansion, retreat, and colonisation influenced by and with feedback on physical-environmental drivers. The model is applied in a schematized mixed fluvial-tidal deltaic mangrove forest in dominantly muddy sediment inspired by the prograding delta of Porong, Indonesia. Model results successfully reproduce observed mangrove extent development, age-height relationship, and morphodynamic delta features.
It is wise to have the git installed in your PC.
You can directly download the executable in WIindows system through this link, or refer to the Git official website for other information.
To run the model, it is advised to create a virtual environment with Anaconda. We have prepared the explicit text file containing the spec list.
First, clone the main repository or download the ZIP file.
Change the working directory to the repo location.
In the current working directory, run:
conda create --name dfmfon --file spec-virtual_env.txt
Once it is finished, activate the newly created virtual environment and install the BMI Python for Delft3D FLexible Mesh
conda activate dfmfon
pip install bmi-python
Now all the required packages have been installed and you are all set to run the DFMFON model. Always make sure to activate the DFMFON environment.
An example to run DFMFON is provided in the `example' folder.
We provide run_example to try the tool and folder template, which you can use for your repeatable runs.
DFMFON currently has two main script, 01_prep_run.py and 02_DFMFON_run.py.
At first, open 01_prep_run.py in your favorite IDE, I suggest Spyder. Adjust Input Folder and Files section to refer to your local directory. Description of each variable:
PROJ_HOME : main location of your run
SYS_APP : location of your FnD3D folder, I suggest to always copy the folder under PROJ_HOME folder
D3D_HOME : location of your Delft3D Flexible Mesh executables
gdal_loc : location of your gdal installation, usually it is located inside your python virtual environment folder
JAVA_Exe : location of your Java Emulator
Mangr_SHP : mangrove shapefile name
D3D_Model : folder name of your D3D run, always put under
Model-Execute\D3DFMD3D_Domain : name of your DFM domain
Additionally, you can adjust another variable, following your specific model needs.
EPSG_Project, x_res, y_res, LLWL
After conducting the Preparation Run, you should have the first MFON simulation and the outputs.
You can copy-paste similar files and folders location of your local run as in 01_prep_run.py to 02_DFMFON_run.py.
Complete the information of config_xml and mdu_file.
Congratulations, you will be ready for the full run of DFMFON model.