Commit 0d101236 authored by Sævik Pål Næverlid's avatar Sævik Pål Næverlid
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Improve documentation

parent 8fb82f7e
......@@ -41,10 +41,12 @@ subpackage folders.
1. Copy `ladim.yaml` and `particle.rls` from the IBM subpackage of interest
into the working directory.
2. If the `pip` installation step was skipped, the `ibm.py` module must be
2. Make desired changes to the `yaml` and `rls` files. More detailed
instructions are found in the `README.md` file within the subpackage.
3. If the `pip` installation step was skipped, the `ibm.py` module must be
copied as well, and the `ibm.module` entry in `ladim.yaml` must be changed
to `"ibm"`.
3. Run `ladim` and the output is written to `out.nc`.
4. Run `ladim` and the output is written to `out.nc`.
## Add new IBMs
......
# Salmon lice
The module represents salmon lice having a vertical swimming behaviour, and
matures at individual rates due to ambient temperature conditions.
The module represents salmon lice having a vertical swimming behaviour due to
ambient light and salt conditions.
The model is based on a number of scientific works on salmon lice behaviour.
Vertical migration is based on [Myksvoll et al. (2011)](http://dx.doi.org/10.1080/19425120.2011.595258).
Maturation is based on [Myksvoll et al. (2011)](http://dx.doi.org/10.1080/19425120.2011.595258).
The model is based on a number of scientific works on salmon lice behaviour, including
- [Author et al. (2011)](http://dx.doi.org/doicode_here)
- New salinity model: [Author et al. (2011)](http://dx.doi.org/doicode_here)
## Usage
......@@ -17,9 +17,9 @@ Common changes applied to `ladim.yaml`:
- Forcing input file (`gridforce.input_file`)
- Vertical diffusion parameter (`ibm.vertical_mixing`)
- Horizontal diffusion parameter (`numerics.diffusion`)
- Egg diameter (`ibm.egg_diam`)
- Time step length (`numerics.dt`)
- Output frequency (`output_variables.outper`)
- Salinity model (`ibm.salinity_model`)
The file `particles.rls` is a tab-delimited text file containing particle
release time and location, as well as particle attributes at the release time.
......@@ -36,8 +36,7 @@ The simulation result is stored in a file specified by the `files.output_file`
entry in `ladim.yaml`. The output variables are specified by the
`output_variables` entries.
## SVIM example
## Real-world example
An example of configuration file and release file used in a real scenario is
provided by `svim_ladim.yaml` and `svim_particles.rls`. The code used to make
the release file is provided by `svim_make_release.m`.
provided by `anne2019_ladim.yaml` and `anne2019_particles.rls`.
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