Python front-end (pyfabm)

FABM comes with a pyfabm package for the python programming language. This package enables you to access FABM’s biogeochemical models directly from python. For instance, you can enumerate a model’s parameters and variables, or obtain temporal derivatives and diagnostics for any given environment and model state. In combination with a python-based time integration scheme (e.g., scipy.integrate.odeint), this also allows you to perform model simulations. More information about pyfabm can be found on the FABM wiki page. Below you can find brief instructions on how to use pyfabm with ERSEM.

Running pyfabm tutorial

To demonstrate how pyfabm can be used with ERSEM, we will calculate the oxygen saturation concentration as a function of temperature and salinity using the method implemented in ERSEM, which is taken from [3].

Note

The following script requires matplotlib to be installed. This can easily be done via pip in the following way:

python -m pip install matplotlib

With pyfabm installed, this can be achieved using the following code:

import matplotlib.pylab as plt
import numpy as np
import os
import pyfabm
import yaml
import tempfile

def main():
    """
    Run pyfabm-ERSEM tutorial

    :param model_path: Full path to netCDF model output
    :type model_path: str

    :return: list of oxygen saturation concentrations
    :rtype: list
    """
    dir_path = os.path.dirname(os.path.realpath(__file__))
    ersem_dir = os.path.dirname(os.path.dirname(dir_path))

    # Path to ERSEM yaml file
    ersem_yaml_file = os.path.join(ersem_dir,
                                   'testcases',
                                   'fabm-ersem-26.02-dvm.yaml')

    if not os.path.isfile(ersem_yaml_file):
        raise RuntimeError("Could not find Ersem yaml file with the "
                           "{}".format(ersem_yaml_file))


    # Removing DVM from pyfabm tests
    with open(ersem_yaml_file) as f:
        raw = f.read()

    data = yaml.safe_load(raw.replace('\t', '  '))
    del data["instances"]["dm"]
    del data["instances"]["dw"]
    del data["instances"]["db"]

    with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as tmp:
        yaml.safe_dump(data, tmp, sort_keys=False)
        temp_path = tmp.name

    # Create model
    model = pyfabm.Model(temp_path)

    # Configure the environment
    model.findDependency('longitude').value = -4.15
    model.findDependency('latitude').value = 50.25
    model.findDependency('number_of_days_since_start_of_the_year').value = 0.
    model.findDependency('temperature').value = 10.
    model.findDependency('wind_speed').value = 1.
    model.findDependency('surface_downwelling_shortwave_flux').value = 50.
    model.findDependency('practical_salinity').value = 35.
    model.findDependency('pressure').value = 10.
    model.findDependency('density').value = 1035.
    model.findDependency('mole_fraction_of_carbon_dioxide_in_air').value = 280.
    model.findDependency('absorption_of_silt').value = 0.07
    model.findDependency('bottom_stress').value = 0.
    model.findDependency('cell_thickness').value = 1.
    model.setCellThickness(1)

    # Verify the model is ready to be used
    assert model.checkReady(), 'One or more model dependencies have not been fulfilled.'

    # Define ranges over which temperature and salinity will be varied
    n_points = 50
    temperature_array = np.linspace(5, 35, n_points)
    salinity_array = np.linspace(25, 45, n_points)

    # Create an array in which to store oxygen_saturation_concentrations
    oxygen_saturation_concentration = np.empty((n_points, n_points), dtype=float)

    # Calculate oxygen saturation concentrations using ERSEM
    for t_idx, t in enumerate(temperature_array):
        model.findDependency('temperature').value = t
        for s_idx, s in enumerate(salinity_array):
            model.findDependency('practical_salinity').value = s
            _ = model.getRates()
            oxygen_saturation_concentration[t_idx, s_idx] = \
                    model.findDiagnosticVariable('O2/osat').value

    # Create the figure
    figure = plt.figure()
    axes = plt.gca()

    # Set color map
    cmap = plt.colormaps.get_cmap('YlOrRd')

    # Plot
    plot = axes.pcolormesh(salinity_array,
                           temperature_array,
                           oxygen_saturation_concentration,
                           shading='auto',
                           cmap=cmap)

    axes.set_xlabel('Salinity (psu)')
    axes.set_ylabel('Temperature (deg. C)')



    # Add colour bar
    cbar = figure.colorbar(plot)
    cbar.set_label('O$_{2}$ (mmol m$^{-3}$)')

    plt.show()

    return oxygen_saturation_concentration

if __name__ == "__main__":
    main()

In additions, example Jupyter notebooks that use the Python front-end can be found in <FABMDIR>/testcases/python and more examples can be found on the FABM wiki.