Repository to do simulations, post-processing and exploratory analyses of the MSc project Integrating physical transport and biological growth of Sargassum in a Lagrangian framework. The specific files of the thesis' figures are listed below. Note that this repository also contains older simulations files.
The NOTEBOOK.ipynb file guides you through (part of) the process of modelling growth of Sargassum rafts during transport in the Atlantic Ocean.
It specifically contains a customizable Sargassum growth model that can be included in Lagrangian simulations using Parcels.
Variables as maximum growth rate and optimal temperature can therefore be easily adapted in this growth model. The notebook is build up by the following steps:
- Defining the limitation functions on growth by physico-chemical factors
- Creating a map of Sargassum locations based on satellite detections from the Sargassum Watch System (SaWS)
- Combining all the required data fields for Sargassum simulation as a fieldset
- Defining Sargassum rafts as particles for a simulation with related characteristic variables
- Setting up the operational kernels to describe Sargassum behaviour
- Executing the simulation
- Visualizing the output
The following list indicates in which files the output processing and visualization of the thesis figures can be found.
For the results, the specific folder in data_Elena on Lorenz where certain particlesets (used in notebook) can be found is also added.
- Figure 2.2:
LIMITATION_ANALYSIS.ipynb
- Figure 3.1:
check_stokes_kernels.ipynb - Figure 3.2:
LIMITATION_ANALYSIS.ipynb - Figure 3.3:
grid_initialization_notebook.ipynb
- Figure 4.1:
check_feedbacks.ipynb& particlesets inSatellite_outandFINAL - Figure 4.2:
OUTPUT_POSTPROCESSING/Output_kN.ipynb& particlesets inSatellite_out - Figure 4.3:
OUTPUT_POSTPROCESSING/Output_kN.ipynb& particlesets inSatellite_out - Figure 4.4:
OUTPUT_POSTPROCESSING/Output_kN.ipynb& particlesets inSatellite_out - Figure 4.5:
OUTPUT_POSTPROCESSING/Output_kN.ipynb& particlesets inSatellite_out - Figure 4.6:
OUTPUT_POSTPROCESSING/Output_kN.ipynb& particlesets inSatellite_out - Figure 4.7:
OUTPUT_POSTPROCESSING/Output_12months.ipynb& particlesets inFINAL - Figure 4.8:
OUTPUT_POSTPROCESSING/Output_12months.ipynb& particlesets inFINAL - Figure 4.9:
OUTPUT_POSTPROCESSING/Output_12months.ipynb& particlesets inFINAL - Figure 4.10:
OUTPUT_POSTPROCESSING/Output_12months.ipynb& particlesets inFINAL - Figure 4.11:
LIMITATION_ANALYSIS.ipynb - Figure 4.12:
check_feedbacks.ipynb& particlesets inSatellite_outandFINAL
- Figure A.1:
OUTPUT_POSTPROCESSING/Output_12months.ipynb& particlesets inFINAL - Figure A.2:
OUTPUT_POSTPROCESSING/Output_12months.ipynb& particlesets inFINAL - Figure A.3:
OUTPUT_POSTPROCESSING/Output_12months.ipynb& particlesets inFINAL - Figure B.1:
OUTPUT_POSTPROCESSING/Output_12months.ipynb& particlesets inFINAL - Figure C.1:
OUTPUT_POSTPROCESSING/Output_12months.ipynb& particlesets inFINAL