LADiM configuration

The LADiM model system is highly configurable using a separate configuration file. The goal is that a user should not have to touch the code, every necessary aspect should be customizable by the configuration file.

The name of the configuration file is given as a command line argument to the main ladim script. If the name is missing, a default name of ladim.yaml is supposed.

It is a goal to provide sane defaults in the configuration file, so that enhancements of the configuration setup do not break existing configuration files.

The configuration file format is a subset of yaml (YAML Ain’t Markup Language). Knowledge of yaml is not necessary. The example configuration files are self-describing and can easily be modified.

Note

The indentation in a yaml file is mandatory, it is part of the syntax. In particular note that the indentation has to be done by spaces, not tabs. Reasonable editors will recognize yaml-files by the extension and will automatically produce spaces when you hit the tab key.

See also

Module configuration

Documentation of the configuration module

An example configuration file

Below is an example configuration file, models/salmon_lice/ladim.yaml.

# Configuration file for salmon lice model using ROMS output

time_control:
    # Start and stop of simulation
    start_time     : 2015-04-01 00:00:00
    stop_time      : 2015-04-01 12:00:00
    # reference_time is optional. default = start_time
    reference_time : 2015-01-01

files:
    particle_release_file : salmon_lice.rls
    output_file           : out.nc
    # For warm start, the warm_start_file goes here

gridforce:
    # Module name is mandatory.
    # The other items are module dependent
    module: ladim.gridforce.ROMS
    # An optional grid_file name can be given
    # Here using the default = first input file
    # grid_file: /scratch/Data/NK800/file_0000.nc
    input_file: /scratch/Data/NK800/file_????.nc
    # subgrid format [i0, i1, j0, j1]
    subgrid: [200, 750, 300, 900]
    # Any extra forcing besides horizontal velocity
    ibm_forcing: [temp, salt]

# IBM section is optional
# When using an IBM the module name is mandatory
# The optional item variables is standardized, default = []
# Other items are module dependent
ibm:
    module: ladim.ibms.ibm_salmon_lice
    variables: [super, age]

particle_release:
    # Discrete or continuous release in time
    release_type: continuous
    # Frequency of continuous particle release, ignored if discrete
    release_frequency: [1, h]   # Hourly release
    # List of variables in the release file
    variables: [mult, release_time, X, Y, Z, farmid, super]
    # Converters (for variables that are not float)
    mult: int
    release_time: time   # np.datetime64[s]
    farmid: int
    # Mark variables as time independent
    particle_variables: [release_time, farmid]

output_variables:
    # Frequency of output
    outper: [1, h]    # Output every hour
    # Variables included in output
    particle: [release_time, farmid]
    instance: [pid, X, Y, Z, super, age]
    # NetCDF arguments
    # format string and attributes
    release_time:
        ncformat: f8   # 64 bit float
        long_name: particle release time
        # Reference_time becomes substituted with value set above
        units: seconds since reference_time
    farmid: {ncformat: i4, long_name: fish farm location number}
    pid: {ncformat: i4, long_name: particle identifier}
    X: {ncformat: f4, long_name: particle X-coordinate}
    Y: {ncformat: f4, long_name: particle Y-coordinate}
    Z:
        ncformat: f4
        long_name: particle depth
        standard_name: depth_below_surface
        units: m
        positive: down
    age:
        ncformat: f4
        long_name: particle age in degree-days
        units: Celcius days
        standard_name: integral_of_sea_water_temperature_wrt_time
    super: {ncformat: f4, long_name: number of individuals in instance}

numerics:
    # Model time step
    dt: [600, s]     # Format = [value, unit]
    # Advection method, EF, RK2, or RK4
    advection: RK2   # Second order Runge Kutta
    # Horizontal random walk diffusion coefficient
    # omit or set to zero if no diffusion
    diffusion: 10    # [m/s**2]