ROMS 3D Ichthyop configuration file
Predefined parameters for ROMS dataset from NetCDF files.
3.3
Main/Time
app.time
Set the general time options of the simulation.
initial_time
Beginning of simulation
year 2019 month 11 day 12 at 12:00
date
Set the beginning date and time of the simulation. Format: year #### month ## day ## at HH:mm.
transport_duration
Transport duration
00071 day(s) 00 hour(s) 00 minute(s)
duration
Set the duration of particle transport. Format: #### day(s) ## hour(s) ## minute(s)
keep_drifting
Particle keep drifting
false
true
boolean
Determine whether a particle should be deactivated or on the contrary should keep drifting once its age exceeds transport duration. This parameter only operates with several release events (see section release schedule) when the simulation duration is upper than the transport duration.
time_step
Time step [second]
1800
integer
The computational time step (dt) expressed in seconds. Take great care for setting this parameter. Simulation must not break the CFL criterion: (U * dt) / dX inferior to 1 with U the velocity and dX the move. An acceptable estimation could be dt = 0.7 * dGrid / Umax with dGrid the average length of the grid cells and Umax the order of magnitude of the fastest current velocities in the hydrodynamic model.
calendar_type
Type of calendar
Gregorian calendar
combo
Climatology calendar
Gregorian calendar
Gregorian calendar
Choose the type of calendar for converting the time variable of the hydrodynamic model (expressed in seconds) into human readble time format. Climatology calendar: 360 days per year. Gregorian calendar: the usual calendar. If you do not know, just skip it ! It is a "cosmetic" parameter that does not affect the run of the simulation. It only controls the display of time on screen.
time_origin
Origin of time
year 2000 month 01 day 01 at 00:00
date
year 1900 month 01 day 01 at 00:00
This parameter comes with Gregorian type of calendar only. For hydrodynamic models that record time variable according to a Gregorian calendar, time is the number of seconds elapsed since an origin of time. Most of the time, origin of time starts 1900/01/01 00:00. Nevertheless, for some simulations, you may have to set another origin of time for the Gregorian calendar. This origin is usually defined as an attribute of the time variable in the hydrodynamic dataset.
time_arrow
Direction of the simulation
forward
combo
backward
forward
forward
Run the simulation backward or forward in time. Ichthyop advection schemes are not 'centered in time' which raises some questions for backtracking. Please refer to the userguide for details.
app.output
Block of options that controls the record of the particle tracks in NetCDF ouput files.
Main/Output
file_prefix
Prefix of the NetCDF output file
roms3d
my-simulation
Type the prefix of the simulation output file. The output filename will look like your-prefix_ichthyop-runYYYYMMDDHHmm.nc, with YYYYMMDDHHmm the current time when running the simulation.
output_path
Output path
/home/lgaravelli/Ichthyop_Runs_Cluster/Bonefish_Abaco_20191112_on_20210406/Ichthyop_Output/
path
output
Select the folder where the simulation NetCDF output file should be saved. For instance, relative paths 'output' or 'output/' or './output' or './output/' are supported and equivalent. They will be interpretated as /path_from_where_you_run_ichthyop/ouput/ If ouput folder does not exist, application will attempt to create it.
record_frequency
Record frequency
6
integer
4
Lagrangian model runs with its own computational time-step, set in the 'time option block'. You may not need to record every step of the simulation in the NetCDF output file. Set the record frequency as a number of computational time-steps. For instance, let's take dt = 1800s and record frequency = 6. Particle positions will be recorded every 3 hours (1800 * 6 = 10800s = 3h) in the NetCDF output file.
trackers
Variable tracking
list
"salinity"
Name of some extra variables you wish to track during the simulation. It must exactly match the name of the corresponding variable in the hydrodynamic dataset. By default, the application records time, longitude, latitude, depth and mortality. For instance, if you wish to track temperature and salinity at particle location, you should type here the names of temperature and salinity variables as they are declared in the hydrodynamic dataset. E.g: "TEMP" "SALT". Some actions will also automatically tracks some additional variables: for instance Linear growth process will track particle length and particle biological stage ((as long as it is enabled, for sure). It will always be explicitly reminded in the description of each action.
dataset.roms_3d
Main/ROMS 3D
Block of options for managing the hydrodynamic dataset. Pre-defined block for ROMS model (Rutgers or UCLA), 3D simulation and local NetCDF files.
input_path
Input path
/home/lgaravelli/Ichthyop_Runs_Cluster/Bonefish_Abaco_20191112_on_20210406/Ichthyop_Param_Files/Hydrography
input
path
Folder containing the ROMS NetCDF files. Relative pathnames are supported. For instance, 'input' or 'input/' or './input' or './input/' are equivalent. Notice the application ignores the subfolders and can only "see" the files located in this folder that matches the "File filter".
file_filter
File filter
GOM_NCOM_2019_06_01-2020_06_01_interp.nc
*.nc
Filename filter. Accepted metacharacters * (for any String) and ? (for any single character). Let's say the input files you want to use for the simulation are in a folder with many other files (not necessarily NetCDF format), but they all have the same prefix. Your file filter will look like prefix*.nc
grid_file
Grid file
/home/lgaravelli/Ichthyop_Runs_Cluster/Bonefish_Abaco_20191112_on_20210406/Ichthyop_Param_Files/Grid/Florida_Bahamas_ROMS_Grd_NCOM.nc
file
Separate grid file for ROMS configuration. In some simulations, lon, lat and mask are archived in separate grid file. In most cases this parameter should be empty.
skip_sorting
Skip NetCDF file sorting
false
false
boolean
Ichthyop chronologically sorts the list of NetCDF input files by comparing the first value of the time variable of each file. Depending on the number of files, the speed for accessing and reading the files, the sorting might take very long time at simulation setup. If the files are already chronologically sorted thanks to their names, you should skip the sorting to increase performance.
shrink_domain
Shrink simulated domain
false
false
boolean
Shrink the size of the domain for running the simulation. It avoids to download the whole data when you are working on a localized area. If "true", you must define the coordinates of the Northwest corner and the Southeast corner of the resized area. If "false", the Northwest corner and the Southeast corner parameters are ignored by the application.
north-west-corner.lat
Latitude of Northwest corner [North degree]
30.00
Set the latitude of Northwest corner for resizing the simulated domain. You can change the coordinate format when editing the value.
lonlat
0.0
north-west-corner.lon
Longitude of Northwest corner [East degree]
-81.30
Set the longitude of Northwest corner for resizing the simulated domain. You can change the coordinate format when editing the value.
lonlat
0.0
south-east-corner.lat
Latitude of Southeast corner [North degree]
24.58
Set the latitude of Southeast corner for resizing the simulated domain. You can change the coordinate format when editing the value.
lonlat
0.0
south-east-corner.lon
Longitude of Southeast corner [East degree]
-76.08
Set the longitude of Southeast corner for resizing the simulated domain. You can change the coordinate format when editing the value.
lonlat
0.0
field_dim_eta
Dimension in the ETA-direction
eta_rho
eta_rho
Name of the NetCDF dimension in the hydrodynamic dataset.
field_dim_xi
Dimension in the XI-direction
xi_rho
xi_rho
Name of the NetCDF dimension in the hydrodynamic dataset.
field_dim_z
Dimension in the vertical direction
s_rho
s_rho
Name of the NetCDF dimension in the hydrodynamic dataset.
field_dim_time
Dimension in time
time
time
Name of the NetCDF dimension in the hydrodynamic dataset.
field_var_bathy
Bathymetry at Rho points
h
h
Name of the NetCDF variable in the hydrodynamic dataset.
field_var_lat
Latitude of Rho points
lat_rho
lat_rho
Name of the NetCDF variable in the hydrodynamic dataset.
field_var_lon
Longitude of Rho points
lon_rho
lon_rho
Name of the NetCDF variable in the hydrodynamic dataset.
field_var_mask
Mask on Rho points
mask_rho
mask_rho
Name of the NetCDF variable in the hydrodynamic dataset.
field_var_pm
Curvilinear coordinate metric in XI
pm
pm
Name of the NetCDF variable in the hydrodynamic dataset.
field_var_pn
Curvilinear coordinate metric in ETA
pn
pn
Name of the NetCDF variable in the hydrodynamic dataset.
field_var_time
Averaged time since initialization
scrum_time
scrum_time
Name of the NetCDF variable in the hydrodynamic dataset.
field_var_zeta
Averaged free-surface
zeta
zeta
Name of the NetCDF variable in the hydrodynamic dataset.
field_var_u
U-momentum component
u
u
Name of the NetCDF variable in the hydrodynamic dataset.
field_var_v
V-momentum component
v
v
Name of the NetCDF variable in the hydrodynamic dataset.
field_csr
S-coordinate stretching curves at Rho points
Cs_r
Cs_r
Name of the NetCDF field in the hydrodynamic dataset (global attribute or variable depending on whether it is UCLA or Rutgers version).
field_csw
S-coordinate stretching curves at W-points
Cs_w
Cs_w
Name of the NetCDF field in the hydrodynamic dataset (global attribute or variable depending on whether it is UCLA or Rutgers version).
field_hc
S-coordinate critical depth
hc
hc
Name of the NetCDF field in the hydrodynamic dataset (global attribute or variable depending on whether it is UCLA or Rutgers version).
class_name
Java Class file
org.previmer.ichthyop.dataset.Roms3dDataset
org.previmer.ichthyop.dataset.Roms3dDataset
class
The Java class called by the application to implement this dataset.
release.stain
Main/Release stain
Block of options for releasing a "stain" of particles aroung a given location.
true
number_particles
Number of particles
10000
1000
integer
Number of particles released in the stain. If several release events are defined (see section release schedule), this parameter becomes the number of particles released in the stain per release event. It means the application will total number_particles_released_in_zones * number_release_events particles.
lon_stain
Longitude [East degree]
-77.27543
17
lonlat
Longitude [East degree] of the stain. You can change the coordinate format when editing the value.
lat_stain
Latitude [North degree]
25.87756
-33
lonlat
Latitude [North degree] of the stain. You can change the coordinate format when editing the value.
depth_stain
Depth [meter]
99.15
-20.0
float
Depth [meter] of the stain. The parameter is ignored for 2D simulation. Positive depth is automatically converted by the application (depth = -depth)
radius_stain
Radius of the stain [meter]
150.0
2000.0
float
Radius [meter] of the stain. Particles are randomly released (for homogeneous distribution) within the circle defined by this radius.
thickness_stain
Thickness of the stain [meter]
31.85
10.0
float
Thickness [meter] of the stain. This parameter is ignored for 2D simulation. Particles are randomly released within the layer [depth_stain - thickness / 2; depth_stain + thickness / 2]
class_name
Java Class file
class
org.previmer.ichthyop.release.StainRelease
org.previmer.ichthyop.release.StainRelease
The Java class called by the application to implement this release process.
Advanced/Transport/General
app.transport
Set the general transport options of the simulation.
coastline_behavior
Coastline behavior
Beaching
Beaching
combo
None
Beaching
Bouncing
Standstill
Determines what should be the behavior of a particle in case a move would take it inland : either it stands still, either it beaches, either it bounces on the coasline as a billiard ball.
action.advection
Options that control the advection process.
Advanced/Transport/Advection
true
scheme
Numerical scheme
Forward Euler
Forward Euler
combo
Forward Euler
Runge Kutta 4
Use a Forward Euler scheme or a Runge-Kutta 4th order scheme.
horizontal
Horizontal advection
true
true
boolean
Determine whether horizontal advection is enabled.
vertical
Vertical advection
true
true
boolean
Determine whether vertical advection is enabled. For 2D simulations, this parameter is ignored.
class_name
Java Class file
org.previmer.ichthyop.action.AdvectionAction
org.previmer.ichthyop.action.AdvectionAction
class
The Java class called by the application to implement this action.
priority
priority
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
high
high
combo
lowest
low
normal
high
highest
action.hdisp
Block of options that control the horizontal dispersion process. Horizontal dispersion has been implemented following Peliz et al. (2007)
Advanced/Transport/Horizontal dispersion
true
epsilon
Dissipation rate [meter2/second3]
1.23457E-8
In the horizontal dispersion model, Peliz defined a lagrangian horizontal diffusion coefficient Kh = pow(epsilon, 1/3) * pow(l, 4/3), following Monin and Ozmidov 1981, with epsilon the turbulent dissipation rate [meter2/second3] and l the lenght of the grid cell (l is determined by the application). Monin and Ozmidov suggested epsilon = 1e-9. Make sure you have read and understood Monin and Ozmidov's paper before changing this value.
float
1E-9
class_name
Java Class file
org.previmer.ichthyop.action.HDispAction
org.previmer.ichthyop.action.HDispAction
class
The Java class called by the application to implement this action.
priority
priority
normal
normal
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.buoyancy
Block of options that control the buoyancy process. This block can be enabled for 3D simulations only. It requires sea water salinity and sea water temperature fields to compute sea water density. Do not activate this process unless you know that the hydrodynamic dataset provides both variables.
Advanced/Transport/Buoyancy
true
particle_density
Particle density [g/cm3]
1.025
float
1.025
Particle density [g/cm3]. Basically, if density is superior to sea water density, particle will sink, if density is inferior to sea water density, particle will go up to the surface. If you want to force particles to keep close surface, take density = 0.9, for instance. This parameter is ignored when a density file (density as age function, refer to next parameter for details) is provided.
density_file
Density file
/home/lgaravelli/Ichthyop_Runs_Cluster/Bonefish_Abaco_20191112_on_20210406/Ichthyop_Param_Files/Density/bonefish_lepto_density.xml
textfile
density_function.csv
Particle density as an age function. The parameter is the pathname of CSV file (semicolon separator) that contains two columns. Headers Time(hour);Density(g/cm3). If this parameter is left void, ichthyop assumes constant particle density.
age_max
Maximum age [day]
41.0
float
3.0
Maximum age [day] for adding buoyancy effect to the particle. If the growth process is activated (see Biology/Growth), this parameter is ignored by the application and the buoyancy only operates during the egg stage.
salinity_field
Salinity variable name
salinity
salt
The name of the salinity variable (case sensitive) in the hydrodynamic dataset.
temperature_field
Temperature variable name
temperature
temp
The name of the temperature variable (case sensitive) in the hydrodynamic dataset.
class_name
Java Class file
org.previmer.ichthyop.action.BuoyancyAction
org.previmer.ichthyop.action.BuoyancyAction
class
The Java class called by the application to implement this action.
priority
priority
normal
normal
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.swimming
Block of options that control the random swimming process. Swimming velocities are provided in a CSV file as an age function of the particle.
Advanced/Transport/Swimming
false
velocity_file
Swimming velocity file
textfile
velocity_function.csv
Particle swimming velocity as an age function. The parameter is the pathname of CSV file (semicolon separator) that contains two columns. Headers Age(day);Velocity(m/s).
constant_velocity
Constant swiming velocity
true
true
boolean
If TRUE the particles will swim at the velocity defined in the CSV file. If FALSE the particles will swim with random velocity between zero and 2 times the velocity defined in the CSV file.
class_name
Java Class file
org.previmer.ichthyop.action.SwimmingAction
org.previmer.ichthyop.action.SwimmingAction
class
The Java class called by the application to implement this action.
priority
priority
normal
normal
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.migration
Block of options to control the Diel Vertical Migration (DVM) process of larvae. Only operate for 3D simulation. We impose deterministic pattern in which organisms reside at different depths at daytime and night-time. User can choose the daytime depth and the night-time depth, in meters. If the growth procedure is activated then the DVM operates during the larvae stages (yolk-sac and feeding larva). If not it operates after a “minimum age”. Setting the daytime depth equal to the night-time depth, the pattern forces the motion of particles at a constant depth.
Advanced/Transport/Vertical migration
true
daytime_depth
Depth at daytime [meter]
-2.0
-30
float
Set the depth [meter] of the particle during daytime. Daytime period starts at sunrise and ends at sunset. Depth is negative number, but the application will automatically convert positive values multiplying by -1. You can set daytime depth = nightime depth to force motion of particle at constant depth.
daytime_depth_file
Depth at daytime as function of age
depth_day.csv
textfile
depth_function.csv
Depth at day time as a function of age. The parameter is the pathname of CSV file (semicolon separator) that contains two columns. Headers Age(day);Depth(metre). Depth is negative number. If this parameter is left void, ichthyop assumes constant daytime depth, defined by parameter "Depth at daytime".
nighttime_depth
Depth at nighttime [meter]
-2.0
-10
float
Set the depth [meter] of the particle during nighttime. Nighttime. period starts at sunset and ends at sunrise. Depth is negative number, but the application will automatically convert positive values multiplying by -1. You can set daytime depth = nightime depth to force motion of particle at constant depth.
nighttime_depth_file
Depth at nighttime as function of age
depth_night.csv
textfile
depth_function.csv
Depth at night as a function of age. The parameter is the pathname of CSV file (semicolon separator) that contains two columns. Headers Age(day);Depth(metre). Depth is negative number. If this parameter is left void, ichthyop assumes constant nighttime depth, defined by parameter "Depth at nighttime".
sunrise
Hour of sunrise [HH:mm]
11:53
hour
07:00
Hour of sunrise [HH:mm], 24 hours format. Make sure that sunrise occurs earlier than sunset.
sunset
Hour of sunset [HH:mm]
22:22
19:00
hour
Hour of sunset HH:mm, 24 hours format. Make sure that sunset occurs later than sunrise.
age_min
Minimum age [day]
41.0
3.5
float
If the growth procedure is activated (See biology section) then the DVM operates during the larvae stages (yolk-sac and feeding larva) and this parameter is ignored by the application. If not migration only operates after this minimum age [day].
class_name
Java Class file
org.previmer.ichthyop.action.MigrationAction
org.previmer.ichthyop.action.MigrationAction
class
The Java class called by the application to implement this action.
priority
priority
normal
normal
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.migration.ontogenetic
Block of options to control the Ontogenetic Vertical Migration (OVM) process of larvae. Only operate for 3D simulation. Based on CMS.
Advanced/Transport/Ontogenetic migration
false
cms_ovm_config_file
Path of the CMS Ontogenetic migration configuration file
file
Select the CSM Ontogenetic migration configuration file.
class_name
Java Class file
org.previmer.ichthyop.action.OntogeneticMigrationAction
org.previmer.ichthyop.action.ntogeneticMigrationAction
class
The Java class called by the application to implement this action.
priority
priority
normal
normal
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.wind
Advanced/Transport/Wind drift
false
Block of options to implement particle drift due to sea surface wind. The application is not able yet to read any realistic wind datasets. You will have to build your own wind scenarii, providing parameters such as wind direction and intensity, windage, etc. in a separate textfile. For 2D simulations, every particle is exposed to surface wind. For 3D simulations, the application only applies wind drift to close-surface particles (technically, particles that reach the top grid level). First time you enable the wind action, do not forget to create a new wind file (the filename is preset but the file may not exist yet on your disk).
wind_file
Wind scenario file
/home/lgaravelli/Ichthyop_Runs_Cluster/Bonefish_Abaco_20191112_on_20210406/Ichthyop_Param_Files/Wind/Output/abaco_wind_20191112_20200122.txt
cfg/my_wind-scenario.txt
textfile
wind-benguela.txt
Select an existing wind scenario (*.txt) or create a new one. Relative pathnames are supported (e.g 'cfg/wind_scenario1.xml' or '../wind_scenario2.xml' etc.).
class_name
Java Class file
class
org.previmer.ichthyop.action.WindAction
org.previmer.ichthyop.action.WindAction
The Java class called by the application to implement this action.
priority
priority
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
normal
normal
combo
lowest
low
normal
high
highest
release.schedule
Block of options to control multi-release events. In most cases, you do not need to define any release schedule, and all the particles are released at the beginning of the simulation (defined in the time section). This option affects the duration of the simulation. Simulation duration is calculated as follow: duration between initial_time and last_release_event plus transport_duration. This ensures that the last released particle will at least be transported for transport_duration. A particle whose age exceeds the duration of transport can as well keep drifting or being “killed” with death cause "old", depending on the value of time section parameter keep_drifting"
Advanced/Release/Schedule
is_enabled
Use release schedule
false
boolean
false
Activate or deactivate the release schedule. If TRUE particles are released according to this release schedule. If FALSE all the particles are relased at the beginning of the simulation (defined in the time section)
events
Release event(s)
year 2019 month 06 day 01 at 06:02
list
Set the dates [year #### month ## day ## at HH:mm] of the release events. You can define as much events as necessary. Just make sure that: 1. the first release events does not occur before the beginning of the simulation, 2. events are defined in chronological order.
release.zone
Advanced/Release/From zones
Block of options for releasing particles within pre-defined geographical zones. This release mode adds a "zone" variable in the NetCDF output file. First time you enable the zone release, do not forget to create a new zone file (the filename is preset but the file may not exist yet on your disk).
false
number_particles
Number of particles
10000
1000
integer
Number of particles released in the zones. The application randomly releases the particles within the zones in order to ensure a homogeneous distribution (= constant concentration of particles among the zones). The downside is that you do not control the number of particles released per zone. If several release events are defined (see section release schedule), this parameter becomes the number of particles released in the zones per release event. It means the application will total number_particles_released_in_zones * number_release_events particles.
zone_file
Zone file
cfg/benguela_zones.xml
cfg/my_zones.xml
zonefile
zone-benguela.xml
Select an existing zone file (*.xml) or create a new one. Relative pathnames are supported (e.g 'cfg/my_zones1.xml' or '../my_zones2.xml' etc.). The application only loads release zones from the file and ignores the other types of zone (recruitment zone for instance).
zone_tracker
Track zones
true
true
boolean
If true the application adds a "zone" variable in the NetCDF output file. Setting to false does not guarantee the "zone" variable will not be recorded in the NetCDF output file because it migt be required by another module (Recruitment for instance).
class_name
Java Class file
org.previmer.ichthyop.release.ZoneRelease
org.previmer.ichthyop.release.ZoneRelease
class
The Java class called by the application to implement this release process.
release.bottom
Advanced/Release/At bottom
Block of options for releasing particles within pre-defined geographical zones at sea bottom. This release mode adds a "zone" variable in the NetCDF output file. First time you enable the zone release, do not forget to create a new zone file (the filename is preset but the file may not exist yet on your disk).
false
number_particles
Number of particles
1000
1000
integer
Number of particles released in the zones. The application randomly releases the particles within the zones in order to ensure a homogeneous distribution (= constant concentration of particles among the zones). The downside is that you do not control the number of particles released per zone. If several release events are defined (see section release schedule), this parameter becomes the number of particles released in the zones per release event. It means the application will total number_particles_released_in_zones * number_release_events particles.
zone_file
Zone file
cfg/benguela_zones.xml
cfg/my_zones.xml
zonefile
zone-benguela.xml
Select an existing zone file (*.xml) or create a new one. Relative pathnames are supported (e.g 'cfg/my_zones1.xml' or '../my_zones2.xml' etc.). The application only loads release zones from the file and ignores the other types of zone (recruitment zone for instance).
zone_tracker
Track zones
true
true
boolean
If true the application adds a "zone" variable in the NetCDF output file. Setting to false does not guarantee the "zone" variable will not be recorded in the NetCDF output file because it migt be required by another module (Recruitment for instance).
class_name
Java Class file
org.previmer.ichthyop.release.BottomRelease
org.previmer.ichthyop.release.BottomRelease
class
The Java class called by the application to implement this release process.
release.patches
Advanced/Release/Patches in zones
false
Block of options for releasing patches of particles within pre-defined geographical zones. It is equivalent to the zone release but instead of releasing single particles, it does release patches of particles. To make a patch, the application release a single particle and then aggregates some particles around the single particle. You can specify the number of patches, the number of particles within a patch and the radius and the thickness of the patches. First time you enable the patches release, do not forget to create a new zone file (the filename is preset but the file may not exist yet on your disk).
number_patches
Number of patches
10
10
integer
Number of patches released in the zones. The application randomly releases the patches within the zones in order to ensure a homogeneous distribution of patches among the zones. The downside is that you do not control the number of patches released per zone.
number_agregated
Number of particles per patch
100
100
integer
The number of aggregated particles in a patch.
radius_patch
Radius of the patch [meter]
2000.0
5000.0
float
Radius of the patch [meter]. If you release large patches within small zones, it is very likely that patches will overlap.
thickness_patch
Thickness of the patch [meter]
2.0
10.0
float
Thickness of the patch [meter]. This parameter is ignored for 2D simulations.
zone_file
Zone file
cfg/benguela_zones.xml
cfg/my_zones.xml
zonefile
zone-benguela.xml
Select an existing zone file (*.xml) or create a new one. Relative pathnames are supported (e.g 'cfg/my_zones1.xml' or '../my_zones2.xml' etc.). The application only loads release zones from the file and ignores the other types of zone recruitment zone for instance).
zone_tracker
Track zones
true
true
boolean
If true the application adds a "zone" variable in the NetCDF output file. Setting to false does not guarantee the "zone" variable will not be recorded in the NetCDF output file because it migt be required by another module (Recruitment for instance).
class_name
Java Class file
class
org.previmer.ichthyop.release.PatchyRelease
org.previmer.ichthyop.release.PatchyRelease
The Java class called by the application to implement this release process.
release.txtfile
Advanced/Release/Drifters from text file
Block of options for releasing particles with initial coordinates pre-defined in a textfile. The application reads the position of the particles in the text file and release them at time "Beginning of simulation". If the Release schedule is activated, the application will repeatedly release the whole bunch of drifters (for each release event).
false
txtfile
Drifter file
cfg/benguela_drifters.txt
cfg/my_drifters.txt
textfile
drifter-benguela.txt
Select an existing drifter textfile (*.txt) or create a new one. Relative pathnames are supported (e.g 'cfg/my_drifters1.xml' or '../my_drifters2.xml' etc.).
class_name
Java Class file
class
org.previmer.ichthyop.release.TxtFileRelease
org.previmer.ichthyop.release.TxtFileRelease
The Java class called by the application to implement this release process.
release.ncfile
Advanced/Release/Restart mode
Block of options for releasing particles with initial coordinates read in an Ichthyop NetCDF output file. The application interpolates the position of the particle in the NetCDF file at time “Beginning of the simulation” or for every "Release event" if the release schedule is activated. It also reads the status of the particle. If the particle had already die, the application releases the particle but it is immediately disabled (not transported). Make sure the time “Beginning of simulation” (or the "Release events") is contained inside the NetCDF file, otherwise the application will crash.
false
ncfile
NetCDF file
file
Select an existing Ichthyop NetCDF output file. Relative pathnames are supported (e.g 'output/ichthyop-run201006291600.nc' or '../ichthyop-run201006291601.nc' etc.).
class_name
Java Class file
class
org.previmer.ichthyop.release.NcFileRelease
The Java class called by the application to implement this release process.
action.lethal_temp
Advanced/Biology/Lethal temperature
true
Block of option for setting up the lower lethal water temperature for the particles. The tool distinguishes between eggs and larvae lethal temperatures when the growth process is activated.
cold_lethal_temperature_egg
Cold lethal temperature (egg) [Celsius degree]
14.0
14.0
float
Lower lethal water temperature [Celsius degree] for the particles. If the growth process is active, this parameter only affects particles at egg stage. This parameter is ignored when a temperature file is provided.
hot_lethal_temperature_egg
Hot lethal temperature (egg) [Celsius degree]
32.0
22.0
float
Higher lethal water temperature [Celsius degree] for the particles. If the growth process is active, this parameter only affects particles at egg stage. This parameter is ignored when a temperature file is provided.
cold_lethal_temperature_larva
Cold lethal temperature (larva) [Celsius degree]
14.0
12.0
float
Lower lethal water temperature [Celsius degree] for particles at larva stage (yolk-sac and feeding larva). This parameter is ignored by the application when the growth process is idle or when a temperature file is provided.
hot_lethal_temperature_larva
Hot lethal temperature (larva) [Celsius degree]
32.0
22.0
float
Higher lethal water temperature [Celsius degree] for particles at larva stage (yolk-sac and feeding larva). This parameter is ignored by the application when the growth process is idle or when a temperature file is provided.
lethal_temp_file
Lethal temperature file
textfile
lethal_temperatures.csv
Lethal temperatures as an age function. The parameter is the pathname of CSV file (semicolon separator) that contains three columns. Headers Time(hour);Cold temp;Hot temp(celsius). Click on new, type a new file name and Ichthyop will generate a CSV template. If this parameter is left void, ichthyop assumes constant lethal temperatures.
temperature_field
Temperature variable name
temperature
temp
The name of the temperature variable (case sensitive) in the hydrodynamic dataset.
temp_tracker
Track temperature
true
true
boolean
If true the application adds a temperature variable in the NetCDF output file. Setting to false does not guarantee the temperature variable will not be recorded in the NetCDF output file because it migt be required by another module.
class_name
Java Class file
org.previmer.ichthyop.action.LethalTempAction
org.previmer.ichthyop.action.LethalTempAction
class
The Java class called by the application to implement this action.
priority
priority
low
low
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.growth
Advanced/Biology/Growth
false
Block of options for setting up the growth model. It simulates the growth in length of particles as a function of water temperature. Length increases linearly with time, at a growth rate that is a linear function of temperature: length(t + dt) = length(t) + (growth_coeff1 + growth_coeff2 * max(temp, threshold_temp)) * dt
coeff1
Growth coefficient 1
0.02
0.02
float
Value of the first coefficient of the growth function (detailed in the block description)
coeff2
Growth coefficient 2
0.03
0.03
float
Value of the second coefficient of the growth function (detailed in the block description)
threshold_temp
Threshold temperature [Celsius degree]
10.0
10.0
float
Threshold temperature [Celsius degree] for the sea water. It ensures that the particles keep growing with a minimum rate, though they are facing colder sea water.
stage_tags
Tags of the stages
"egg" "yolk-sac larva" "feeding larva"
"egg" "yolk-sac" "feeding"
list
Names of each physiological stage of the larva life history. No matter what you set, Ichthyop assumes that the first stage corresponds to egg stage.
stage_thresholds
Initial length of the stages [millimetre]
"0.025" "2.8" "4.5"
"0.025" "2.8" "4.5"
list
Initial length for each physiological stage of the larva life history, in millimetre. Ichthyop assumes that the first length provided corresponds to the egg length.
temperature_field
Temperature variable name
temperature
temp
The name of the temperature variable (case sensitive) in the hydrodynamic dataset.
length_tracker
Track particle length
true
true
boolean
If true the application adds a "length" variable in the NetCDF output file.
stage_tracker
Track particle biological stage
true
true
boolean
If true the application adds a "stage" variable in the NetCDF output file.
class_name
Java Class file
org.previmer.ichthyop.action.LinearGrowthAction
org.previmer.ichthyop.action.LinearGrowthAction
class
The Java class called by the application to implement this action.
priority
priority
low
low
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.growth.sole
Advanced/Biology/Solea growth
false
Block of options for setting up the growth model of Sole larvae. It simulates the growth in length of particles as a function of water temperature. Length increases with time length(t + dt) = length(t) + c1 * (temperature ^ c2) * dt, c1 and c2 depending on the stage of the larvae
temperature_field
Temperature variable name
temperature
temp
The name of the temperature variable (case sensitive) in the hydrodynamic dataset.
stage_tags
Tags of the stages
"egg" "yolk-sac larva" "feeding larva" "metamorphosing larva"
"egg" "yolk-sac larva" "feeding larva" "metamorphosing larva"
list
Names of each physiological stage of the larva life history. No matter what you set, Ichthyop assumes that the first stage corresponds to egg stage.
stage_thresholds
Initial length of the stages [millimetre]
"1.2" "3" "4" "8"
"1.2" "3" "4" "8"
list
Initial length for each physiological stage of the larva life history, in millimetre. Ichthyop assumes that the first length provided corresponds to the egg length.
c1
First coeff of the growth equation
"0.0066" "0.0073" "0.0011" "0.0017"
"0.0066" "0.0073" "0.0011" "0.0017"
list
First coefficient of the sole growth equation, c1, such as dLength(dt) = c1 * (temperature ^ c2) * dt
c2
Second coeff of the growth equation
"1.5739" "1.4619" "1.9316" "1.9316"
"1.5739" "1.4619" "1.9316" "1.9316"
list
Second coefficient of the sole growth equation, c2, such as dLength(dt) = c1 * (temperature ^ c2) * dt
class_name
Java Class file
org.previmer.ichthyop.action.SoleGrowthAction
org.previmer.ichthyop.action.SoleGrowthAction
class
The Java class called by the application to implement this action.
priority
priority
low
low
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.recruitment.zone
Advanced/Biology/Recruitment/In zones
true
Block of options for defining some recruitment criterions and recruitment zones, in order to study, for instance, the recruitment success of a particular geographic area. First time you enable the recruitment process, do not forget to create a new zone file (the filename is preset but the file may not exist yet on your disk).
criterion
Recruitment criterion
Age criterion
Age criterion
combo
Age criterion
Length criterion
Age criterion
Select the type of criterion the application should use to check wheter a particle has been recruited or not. When the growth process is idle, you must use the age based criterion (otherwise application will crash). When growth is taken into account the criterion might also be a minimal length threshold.
limit_age
Recruitment limit age [day]
41.0
7.0
float
A particle must be "older" than the specified age [day] to be considered as recruitable. This parameter is ignored if the recruitment criterion is based on the particle length.
limit_length
Recruitment limit length [millimeter]
6.0
6.0
float
A particle must be "bigger" than the specified length [millimeter] to be considered as recruitable. This parameter is ignored if the recruitment criterion is based on the particle age. Only use this criterion if the growth model is activated.
duration_min
Minimal duration in recruitment zone [day]
1.0
0.0
float
Minimal duration [day] a particle has to spend in a recruitment area to be considered as recruitable.
stop_moving
Stop moving when recruited
true
false
boolean
Force a particle to remain where it is as soon as it is recruited. If activated, the particle could not be recruited in any other recruitment area. On the contrary, a particle that does not stop moving when recruited can keep drifting and being recruited in others recruitment areas, as long as the recruitement conditions are fulfilled.
zone_file
Zone file
/home/lgaravelli/Ichthyop_Runs_Cluster/Bonefish_Abaco_20191112_on_20210406/Ichthyop_Param_Files/Zones/Output/Bahamas_Zones.xml
cfg/my_zones.xml
zonefile
zone-benguela.xml
Select an existing zone file (*.xml) or create a new one. Relative pathnames are supported (e.g 'cfg/my_zones1.xml' or '../my_zones2.xml' etc.). The application only loads recruitment zones from the file and ignores the other types of zone (release zone for instance).
recruited_tracker
Track recruitment status
true
true
boolean
If true the application adds a "recruited" variable in the NetCDF output file.
zone_tracker
Track zones
true
true
boolean
If true the application adds a "zone" variable in the NetCDF output file. Setting to false does not guarantee the "zone" variable will not be recorded in the NetCDF output file because it migt be required by another module (Zone release for instance).
class_name
Java Class file
org.previmer.ichthyop.action.RecruitmentZoneAction
org.previmer.ichthyop.action.RecruitmentZoneAction
class
The Java class called by the application to implement this action.
priority
priority
highest
highest
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.recruitment.stain
Advanced/Biology/Recruitment/In stain
false
Block of options for defining some recruitment criterions and a recruitment stain, in order to study, for instance, the recruitment success of a particular geographic area.
criterion
Recruitment criterion
Age criterion
Age criterion
combo
Age criterion
Length criterion
Age criterion
Select the type of criterion the application should use to check wheter a particle has been recruited or not. When the growth process is idle, you must use the age based criterion (otherwise application will crash). When growth is taken into account the criterion might also be a minimal length threshold.
limit_age
Recruitment limit age [day]
7.0
7.0
float
A particle must be "older" than the specified age [day] to be considered as recruitable. This parameter is ignored if the recruitment criterion is based on the particle length.
limit_length
Recruitment limit length [millimeter]
6.0
6.0
float
A particle must be "bigger" than the specified length [millimeter] to be considered as recruitable. This parameter is ignored if the recruitment criterion is based on the particle age. Only use this criterion if the growth model is activated.
stop_moving
Stop moving when recruited
false
false
boolean
Force a particle to remain where it is as soon as it is recruited. If activated, the particle could not be recruited in any other recruitment area. On the contrary, a particle that does not stop moving when recruited can keep drifting and being recruited in others recruitment areas, as long as the recruitement conditions are fulfilled.
lon_stain
Longitude [East degree]
17
17
lonlat
Longitude [East degree] of the stain. You can change the coordinate format when editing the value.
lat_stain
Latitude [North degree]
-33
-33
lonlat
Latitude [North degree] of the stain. You can change the coordinate format when editing the value.
depth_stain
Depth [meter]
-20.0
-20.0
float
Depth [meter] of the stain. The parameter is ignored for 2D simulation. Positive depth is automatically converted by the application (depth = -depth)
radius_stain
Radius of the stain [meter]
50000.0
2000.0
float
Radius [meter] of the stain. Particles are randomly released (for homogeneous distribution) within the circle defined by this radius.
thickness_stain
Thickness of the stain [meter]
10.0
10.0
float
Thickness [meter] of the stain. This parameter is ignored for 2D simulation. Particles are randomly released within the layer [depth_stain - thickness / 2; depth_stain + thickness / 2]
recruited_tracker
Track recruitment status
true
true
boolean
If true the application adds a "recruited" variable in the NetCDF output file.
class_name
Java Class file
org.previmer.ichthyop.action.RecruitmentStainAction
org.previmer.ichthyop.action.RecruitmentStainAction
class
The Java class called by the application to implement this action.
priority
priority
highest
highest
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.
action.turtle
Advanced/Biology/Turtle move
false
Block of options for modelling turtle moves influenced by earth magnetical field. First time you enable the turtle module, do not forget to create a new zone file (the filename is preset but the file may not exist yet on your disk) or set an existing one.
zone_file
Zone file
cfg/benguela_zones.xml
cfg/my_zones.xml
zonefile
zone-benguela.xml
Select an existing zone file (*.xml) or create a new one. Relative pathnames are supported (e.g 'cfg/my_zones1.xml' or '../my_zones2.xml' etc.). The application only loads orientation zones from the file and ignores the other types of zone (release zone for instance).
class_name
Java Class file
org.previmer.ichthyop.action.TurtleSwimAction
org.previmer.ichthyop.action.TurtleSwimAction
class
The Java class called by the application to implement this action.
priority
priority
normal
normal
combo
lowest
low
normal
high
highest
Level of priority of the action (comparatively to other actions). Each time step, a high priority action will be called by the application before than a low priority action. Actions with same level of priority will be called without any specific order.