ladim-plugins 2.0.0

Plugins for LADiM

Plugins for LADiM

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.

List of available plugins

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

Installation

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.

Usage

1. Copy ladim.yaml and particle.rls from the IBM subpackage of interest into the working directory.
2. Make desired changes to the yaml and rls files. More detailed instructions are found in the README.md file within the subpackage.
3. Run ladim and the output is written to out.nc.

Contribute

To add new plugins, contact the maintainer of the ladim_plugins repository. A properly structured IBM subpackage has the following ingredients:

1. A file __init__.py containing the statement from .ibm import IBM
2. The IBM module itself, named ibm.py
3. A README.md file containing instructions for use
4. A simple test example. This includes a ladim.yaml configuration file, a particles.rls release file, a forcing.nc forcing file (may be copied from another subpackage), and a ladim output file named out.nc.
5. Optionally a test example for generating release files. This includes a release.yaml configuration file and an output release file named out.rls.
6. 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.