aquacrop/solution/germination.py

import numpy as np
from typing import TYPE_CHECKING



if TYPE_CHECKING:
    # Important: classes are only imported when types are checked, not in production.
    from aquacrop.entities.soilProfile import SoilProfile
    from aquacrop.entities.initParamVariables import InitialCondition


def germination(
    InitCond: "InitialCondition",
    Soil_zGerm: float,
    prof: "SoilProfile",
    Crop_GermThr: float,
    Crop_PlantMethod: bool,
    gdd: float,
    growing_season: bool,
    ) -> "InitialCondition":
    """
    Function to check if crop has germinated


    <a href="https://www.fao.org/3/BR248E/br248e.pdf#page=32" target="_blank">Reference Manual: germination condition</a> (pg. 23)


    Arguments:


        InitCond (InitialCondition): InitCond object containing model paramaters

        Soil_zGerm (float): Soil depth affecting germination

        prof (SoilProfile): Soil object containing soil paramaters

        Crop_GermThr (float): Crop germination threshold

        Crop_PlantMethod (bool): sown as seedling True or False

        gdd (float): Number of Growing Degree Days on current day

        growing_season (bool): is growing season (True or Flase)


    Returns:


        NewCond (InitialCondition): InitCond object containing updated model paramaters







    """

    ## Store initial conditions in new structure for updating ##
    NewCond = InitCond

    ## Check for germination (if in growing season) ##
    if growing_season == True:

        if (NewCond.germination == False):
            # Find compartments covered by top soil layer affecting germination
            comp_sto = np.argwhere(prof.dzsum >= Soil_zGerm).flatten()[0]
            # Calculate water content in top soil layer
            Wr = 0
            WrFC = 0
            WrWP = 0
            for ii in range(comp_sto + 1):
                # Get soil layer
                # Determine fraction of compartment covered by top soil layer
                if prof.dzsum[ii] > Soil_zGerm:
                    factor = 1 - ((prof.dzsum[ii] - Soil_zGerm) / prof.dz[ii])
                else:
                    factor = 1

                # Increment actual water storage (mm)
                Wr = Wr + round(factor * 1000 * InitCond.th[ii] * prof.dz[ii], 3)
                # Increment water storage at field capacity (mm)
                WrFC = WrFC + round(factor * 1000 * prof.th_fc[ii] * prof.dz[ii], 3)
                # Increment water storage at permanent wilting point (mm)
                WrWP = WrWP + round(factor * 1000 * prof.th_wp[ii] * prof.dz[ii], 3)

            # Limit actual water storage to not be less than zero
            if Wr < 0:
                Wr = 0

            # Calculate proportional water content
            WcProp = 1 - ((WrFC - Wr) / (WrFC - WrWP))

            # Check if water content is above germination threshold
            if (WcProp >= Crop_GermThr):
                # Crop has germinated
                NewCond.germination = True
                # If crop sown as seedling, turn on seedling protection
                if Crop_PlantMethod == True:
                    NewCond.protected_seed = True
                else:
                    # Crop is transplanted so no protection
                    NewCond.protected_seed = False

            # Increment delayed growth time counters if germination is yet to
            # occur, and also set seed protection to False if yet to germinate
            else:
                NewCond.delayed_cds = InitCond.delayed_cds + 1
                NewCond.delayed_gdds = InitCond.delayed_gdds + gdd
                NewCond.protected_seed = False

    else:
        # Not in growing season so no germination calculation is performed.
        NewCond.germination = False
        NewCond.protected_seed = False
        NewCond.delayed_cds = 0
        NewCond.delayed_gdds = 0

    return NewCond