Official Documentation.

Check our official GitHub pages documentation at https://deltares.github.io/NBSDynamics/.

CoralModel

A biophysical model framework written in Python to make simulations on coral development based on four environmental factors: (1) light; (2) flow; (3) temperature; and (4) acidity. For the hydrodynamics, the model can be coupled to Delft3D Flexible Mesh; a hydrodynamic model developed at Deltares (more information). To enable this online coupling, certain configurations of Python are required (more details).

Note: This model is still in its beta and further development is still being done. coral_model_v0 is used for the study and is rewritten (coral_model) to enhance collaboration. (The original version has not been written efficiently and is hard to follow for outsiders.) More information on this version control here.

Biophysics

This biophysical model framework is part of the result of a master thesis of which the key findings are published in Environmental Modelling and Software (the paper can be found here).

The biophysical relations used in the biophysical model framework are mainly process-based, where for the acidity the proxy of the aragonite saturation state is used. Furthermore, both photo- and thermal-acclimatisation are included, which result in a dynamic behaviour of the corals to their environment. Hence, the corals are modelled such that they can adapt to changing environmental conditions over time.

For more details on the biophysics, reference is made to the master thesis and the paper that substitute this repository.

Python code

The Python code is written in Python 3 and makes use of various packages. Not all of these packages are automatically included in the standard library of Python, such as NetCDF4 (download). In case the biophysical model framework is to be coupled to Delft3d Flexible Mesh, the bmi.wrapper package is also required (download).

The settings of Python and other packages for the online coupling to work properly are the following:

• Python version 3.6.5
• NumPy version 1.14.3
• SciPy version 1.1.0
• NetCDF4 version 1.4.2
• Matplotlib version 2.2.2
• BMI-Python

Note: These requirements are only required in case the biophysical model framework is to be coupled with Delft3D Flexible Mesh.

Version control

There are two versions of the CoralModel: coral_model_v0 and coral_model. The first (coral_model_v0) is the original code as used in the study (i.e. master thesis and paper). The latter (coral_model) is an updated version, which is rewritten such that it enhances collaboration. This collaboration was one of the goals to further develop this model, and the biophysical modelling of coral development.

coral_model_v0 will be depreciated in the future, when coral_model is fully operational and possibly even incorporates more aspects of coral (reef) development.