data/miscanthus_x_giganteus.R

In ebimodeling/biocro: Modular Crop Growth Simulations

miscanthus_x_giganteus <- list(
    direct_modules = list(
        stomata_water_stress = "BioCro:stomata_water_stress_linear",
        "BioCro:leaf_water_stress_exponential",
        "BioCro:parameter_calculator",
        "BioCro:soil_evaporation",
        solar_coordinates = "BioCro:solar_position_michalsky",
        canopy_photosynthesis = "BioCro:c4_canopy",
        partitioning_coefficients = "BioCro:partitioning_coefficient_selector",
        partitioning_growth_calculator = "BioCro:partitioning_growth_calculator"
    ),
    differential_modules = list(
        senescence = "BioCro:thermal_time_senescence",
        "BioCro:partitioning_growth",
        thermal_time = "BioCro:thermal_time_linear",
        soil_profile = "BioCro:two_layer_soil_profile"
    ),
    ode_solver = list(
        type = 'homemade_euler',
        output_step_size = 1.0,
        adaptive_rel_error_tol = 1e-5,
        adaptive_abs_error_tol = 1e-5,
        adaptive_max_steps = 200
    ),
    initial_values = list(
        cws1                        = 0.32,
        cws2                        = 0.32,
        Grain                       = 0,
        Shell                       = 0,
        Leaf                        = 7e-04,
        LeafLitter                  = 0,
        leaf_senescence_index       = 0,
        Rhizome                     = 7,
        RhizomeLitter               = 0,
        rhizome_senescence_index    = 0,
        Root                        = 0.007,
        RootLitter                  = 0,
        root_senescence_index       = 0,
        soil_water_content          = 0.32,
        Stem                        = 0.007,
        StemLitter                  = 0,
        stem_senescence_index       = 0,
        TTc                         = 0
    ),
    parameters = list(
        absorptivity_par            = 0.8,
        alpha1                      = 0.04,
        alphab1                     = 0,
        atmospheric_pressure        = 101325,
        atmospheric_scattering      = 0.3,
        atmospheric_transmittance   = 0.6, # Campbell and Norman, An Introduction to Environmental Biophysics, 2nd Edition, Pg 173
        b0                          = 0.08,
        b1                          = 3,
        beta                        = 0.93,
        Catm                        = 400,
        chil                        = 1,
        et_equation                 = 0,
        Gs_min                      = 1e-3,
        heightf                     = 3,
        hydrDist                    = 0,
        iSp                         = 1.7,
        kd                          = 0.1,
        kGrain1                     = 0,
        kGrain2                     = 0,
        kGrain3                     = 0,
        kGrain4                     = 0,
        kGrain5                     = 0,
        kGrain6                     = 0,
        kLeaf1                      = 0.33,
        kLeaf2                      = 0.14,
        kLeaf3                      = 0.01,
        kLeaf4                      = 0.01,
        kLeaf5                      = 0.01,
        kLeaf6                      = 0.01,
        kparm                       = 0.7,
        kpLN                        = 0.2,
        kRhizome1                   = -8e-04,
        kRhizome2                   = -5e-04,
        kRhizome3                   = 0.35,
        kRhizome4                   = 0.35,
        kRhizome5                   = 0.35,
        kRhizome6                   = 0.35,
        kRoot1                      = 0.3,
        kRoot2                      = 0.01,
        kRoot3                      = 0.01,
        kRoot4                      = 0.01,
        kRoot5                      = 0.01,
        kRoot6                      = 0.01,
        kShell                      = 0,
        kStem1                      = 0.37,
        kStem2                      = 0.85,
        kStem3                      = 0.63,
        kStem4                      = 0.63,
        kStem5                      = 0.63,
        kStem6                      = 0.63,
        lat                         = 40,
        LeafN                       = 2,
        LeafN_0                     = 2,
        leafwidth                   = 0.04,
        leaf_reflectance            = 0.2,
        leaf_transmittance          = 0.2,
        lnfun                       = 0,
        longitude                   = -88,
        lowerT                      = 3,
        minimum_gbw                 = 0.34,
        mrc1                        = 0.02,
        mrc2                        = 0.03,
        nalphab0                    = 0.02367,
        nalphab1                    = 0.000488,
        net_assimilation_rate_shell = 0.0,
        nileafn                     = 85,
        nkln                        = 0.5,
        nkpLN                       = 0.17,
        nlayers                     = 10,
        nlnb0                       = -5,
        nlnb1                       = 18,
        nRdb0                       = -4.5917,
        nRdb1                       = 0.1247,
        nvmaxb0                     = -16.25,
        nvmaxb1                     = 0.6938,
        par_energy_content          = 0.219,
        par_energy_fraction         = 0.5,
        phi1                        = 0.01,
        phi2                        = 10,
        Rd                          = 0.8,
        remobilization_fraction     = 0.6,
        retrans                     = 0.9,
        retrans_rhizome             = 1.0,
        rfl                         = 0.2,
        rsdf                        = 0.44,
        rsec                        = 0.2,
        seneLeaf                    = 3000,
        seneRhizome                 = 4000,
        seneRoot                    = 4000,
        seneStem                    = 3500,
        soil_air_entry              = -2.6,
        soil_bulk_density           = 1.35,
        soil_b_coefficient          = 5.2,
        soil_clay_content           = 0.34,
        soil_clod_size              = 0.04,
        soil_depth1                 = 0.0,
        soil_depth2                 = 2.5,
        soil_depth3                 = 10.0,
        soil_field_capacity         = 0.32,
        soil_reflectance            = 0.2,
        soil_sand_content           = 0.32,
        soil_saturated_conductivity = 6.4e-05,
        soil_saturation_capacity    = 0.52,
        soil_silt_content           = 0.34,
        soil_transmission           = 0.01,
        soil_wilting_point          = 0.2,
        sowing_time                 = 0,
        specific_heat_of_air        = 1010,
        Sp_thermal_time_decay       = 0,
        tbase                       = 0,
        theta                       = 0.83,
        timestep                    = 1,
        tp1                         = 562,
        tp2                         = 1312,
        tp3                         = 2063,
        tp4                         = 2676,
        tp5                         = 3211,
        upperT                      = 37.5,
        vmax1                       = 39,
        vmax_n_intercept            = 0,
        wsFun                       = 2
    )
)