Commit b3175f7a authored by Sævik Pål Næverlid's avatar Sævik Pål Næverlid
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Merge branch 'feature/improve_documentation'

parents 30cb34df 61d5de58
# Boyant eggs
_Brief description goes here._
The module represents fish eggs that have a vertical migration rate due to
buoyancy and vertical turbulence. Advection due to upwelling/downwelling is
not included.
The theoretical foundation for the module is documented by
[Myksvoll et al. (2011)](http://dx.doi.org/10.1080/19425120.2011.595258).
......@@ -27,30 +29,15 @@ within `ladim.yaml`.
Finally, copy `ladim.yaml` and `particles.rls` to a separate directory and
run `ladim` here.
## Output
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
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`.
Start with make_release_egg.m
- choose grid
- choose release locations in grid coordinates
- choose release depth
- choose egg buoyancy
- choose release time
Output is release_svim_egg.rls
Check ibm_egg.py
- choose egg diameter (cod=0.0014, saithe=0.0011)
- specify maximum depth of particles
Check ladim.yaml
- choose start and stop time
- add path to grid and input file
- add name of release file
- ibm_module: 'ibm_egg'
- choose output frequency and multiple files
- choose proper time step and diffusion depending on horizontal resoultion
......@@ -56,24 +56,48 @@ output_variables:
# Variable names
particle: [release_time, group_id]
instance: [pid, X, Y, Z, age, super, egg_buoy ]
# NetCDF arguments
# --- Output format for standard variables ---
# Output format for the particle release time
release_time:
ncformat: f8
long_name: particle release time
units: seconds since reference_time
temp: {ncformat: f4, long_name: temperature}
egg_buoy: {ncformat: f4, long_name: egg buoyancy, units: '1'}
group_id: {ncformat: i4, long_name: particle group id}
pid: {ncformat: i4, long_name: particle identifier}
X: {ncformat: f4, long_name: particle X-coordinate}
Y: {ncformat: f4, long_name: particle Y-coordinate}
# Output format for the particle identifier
pid:
ncformat: i4
long_name: particle identifier
# Output format for the X coordinate
X:
ncformat: f4
long_name: particle X-coordinate
# Output format for the Y coordinate
Y:
ncformat: f4
long_name: particle Y-coordinate
# Output format for the particle depth
Z:
ncformat: f4
long_name: particle depth
standard_name: depth_below_surface
units: m
positive: down
# --- Output format for IBM-specific variables ---
# Output format for the temperature
temp:
ncformat: f4
long_name: temperature
# Output format for the egg buouy
egg_buoy: {ncformat: f4, long_name: egg buoyancy, units: '1'}
group_id: {ncformat: i4, long_name: particle group id}
age:
ncformat: f4
long_name: particle age in degree-days
......
# Sedimentation module
# Sediments
The module represents passive particles that have a vertical migration rate due
to sinking and vertical turbulence. Advection due to upwelling/downwelling is
not included.
Particles that reach the sea floor are immobilized. They are not resuspended.
## Usage
Modify `ladim.yaml` and `particles.rls` to suit your needs.
Common changes applied to `ladim.yaml`:
- Start date of simulation (`time_control.start_time`)
- Stop date of simulation (`time_control.stop_time`)
- Forcing input file (`gridforce.input_file`)
- Horizontal diffusion parameter (`numerics.diffusion`)
- Time step length (`numerics.dt`)
- Output frequency (`output_variables.outper`)
- Vertical diffusion parameter (`ibm.vertical_mixing`)
- Particle life span (`ibm.lifespan`)
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.
The order of the columns is given by the entry `particle_release.variables`
within `ladim.yaml`.
Finally, copy `ladim.yaml` and `particles.rls` to a separate directory and
run `ladim` here.
## Output
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.
......@@ -15,12 +15,15 @@ gridforce:
# Module name is mandatory.
# The other items are module dependent
module: ladim.gridforce.ROMS
input_file: forcing.nc
input_file: forcing.nc # Use wildcards (*) to select a range of files
ibm:
module: ladim_ibm.sedimentation
variables: [sink_vel, active, age]
variables:
- sink_vel # Sinking velocity [m/s]
- active # 1 if mobile, 0 if immobile
- age # Particle age in seconds
lifespan: 200 # Time (seconds) before a particle is taken out of the simulation
vertical_mixing: 0.0001 # [m*2/s]
......@@ -36,25 +39,36 @@ particle_release:
output_variables:
# Frequency of output
outper: [60, s]
# Variables included in output
particle: [release_time]
instance: [pid, X, Y, Z, active]
# NetCDF arguments
# format string and attributes
# --- Output format for standard variables ---
# Output format for the particle release time
release_time:
ncformat: f8 # 64 bit float
ncformat: f8
long_name: particle release time
# Reference_time becomes substituted with value set above
units: seconds since reference_time
pid: {ncformat: i4, long_name: particle identifier}
active: {
ncformat: i4,
long_name: particle active mask,
# flag_values: [0, 1],
flag_meanings: inactive active,
}
X: {ncformat: f4, long_name: particle X-coordinate}
Y: {ncformat: f4, long_name: particle Y-coordinate}
# Output format for the particle identifier
pid:
ncformat: i4
long_name: particle identifier
# Output format for the X coordinate
X:
ncformat: f4
long_name: particle X-coordinate
# Output format for the Y coordinate
Y:
ncformat: f4
long_name: particle Y-coordinate
# Output format for the particle depth
Z:
ncformat: f4
long_name: particle depth
......@@ -62,6 +76,13 @@ output_variables:
units: m
positive: down
# Output format for the particle active indicator
active:
ncformat: i4,
long_name: particle active mask,
# flag_values: [0, 1],
flag_meanings: inactive active,
numerics:
# Model time step
......
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