This repository contains plugins for the Lagrangian Advection and Diffusion Model (LADiM), which is the particle tracking software used at the Institute of Marine Research (IMR). (https://github.com/bjornaa/ladim)
Documentation and examples are provided for each model.
| Name | Description |
|---|---|
| chemicals | Passive tracer |
| egg | Buoyant fish eggs |
| lunar_eel | Glass eels with lunar compass |
| nk800met | Module for utilizing forcing data from the met.no thredds server |
| release | General module for creating release files |
| salmon_lice | Salmon lice larvae |
| sandeel | Sand eel larvae |
| sedimentation | Sinking particles |
| utils | General utility functions for IBMs |
Install using the following commands (the first command can be skipped if LADiM is already present on your system):
pip install git+https://github.com/pnsaevik/ladim.git
pip install git+https://github.com/pnsaevik/ladim_plugins.git
The installation can be tested with the command
pytest -Wignore --pyargs ladim_plugins
This command will run ladim on each of the plugins, using the sample ladim.yaml
and particle.rls files found in the subpackage folders. The tests succeed if
ladim is present on the system, ladim_plugins is installed correctly, and the
output from the ladim runs matches exactly with the out.nc files found in the
subpackage folders.
- Copy
ladim.yamlandparticle.rlsfrom the IBM subpackage of interest into the working directory. - Make desired changes to the
yamlandrlsfiles. More detailed instructions are found in theREADME.mdfile within the subpackage. - Run
ladimand the output is written toout.nc.
To add new plugins, contact the maintainer of the ladim_plugins repository. A
properly structured IBM subpackage has the following ingredients:
- A file
__init__.pycontaining the statementfrom .ibm import IBM - The IBM module itself, named
ibm.py - A
README.mdfile containing instructions for use - A simple test example. This includes a
ladim.yamlconfiguration file, aparticles.rlsrelease file, aforcing.ncforcing file (may be copied from another subpackage), and a ladim output file namedout.nc. - Optionally a test example for generating release files. This includes a
release.yamlconfiguration file and an output release file namedout.rls. - Optionally additional automated test modules, named
test_*.py
An ideal test example should be quick to run and easy to analyze, but still be complicated enough to demonstrate most capabilities of the IBM model. To achieve this, it may be a good idea to use only a few time steps and a few particles at selected positions. In some cases it may also be necessary to specify somewhat unrealistic particle parameters to demonstrate certain features.
The test is run using the command pytest -Wignore --pyargs ladim_plugins. The
test succeeds if ladim is able to run the examples, and the output matches the
contents of out.nc / out.rls.