biocro: Modular Crop Growth Simulations

willow <- 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:c3_canopy",
        partitioning_coefficients = "BioCro:partitioning_coefficient_selector",
        partitioning_growth_calculator = "BioCro:partitioning_growth_calculator"
    ),
    differential_modules = list(
        senescence = "BioCro:thermal_time_and_frost_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                        = 0.02,
        leafdeathrate               = 5,
        LeafLitter                  = 0,
        Rhizome                     = 0.99,
        RhizomeLitter               = 0,
        rhizome_senescence_index    = 0,
        Root                        = 1,
        RootLitter                  = 0,
        root_senescence_index       = 0,
        soil_water_content          = 0.32,
        Stem                        = 0.99,
        StemLitter                  = 0,
        stem_senescence_index       = 0,
        TTc                         = 0
    ),
    parameters = list(
        absorptivity_par             = 0.8,
        alpha1                       = 0,
        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                           = 5,
        beta_PSII                    = 0.5,
        Catm                         = 400,
        chil                         = 1,
        electrons_per_carboxylation  = 4.5,
        electrons_per_oxygenation    = 5.25,
        growth_respiration_fraction  = 0.3,
        Gs_min                       = 1e-3,
        heightf                      = 3,
        hydrDist                     = 0,
        iSp                          = 1.1,
        jmax                         = 180,
        kd                           = 0.37,
        kGrain1                      = 0,
        kGrain2                      = 0,
        kGrain3                      = 0,
        kGrain4                      = 0,
        kGrain5                      = 0,
        kGrain6                      = 0,
        kLeaf1                       = 0.98,
        kLeaf2                       = 0.98,
        kLeaf3                       = 0.15,
        kLeaf4                       = 0.15,
        kLeaf5                       = 1e-05,
        kLeaf6                       = 1e-06,
        kpLN                         = 0.2,
        kRhizome1                    = -8e-04,
        kRhizome2                    = 0.007,
        kRhizome3                    = 0.105,
        kRhizome4                    = 0.105,
        kRhizome5                    = 0.15,
        kRhizome6                    = 0.15,
        kRoot1                       = 0.01,
        kRoot2                       = 0.003,
        kRoot3                       = 0.045,
        kRoot4                       = 0.045,
        kRoot5                       = 0.15,
        kRoot6                       = 0.15,
        kShell                       = 0,
        kStem1                       = 0.01,
        kStem2                       = 0.01,
        kStem3                       = 0.7,
        kStem4                       = 0.7,
        kStem5                       = 0.7,
        kStem6                       = 0.7,
        lat                          = 40,
        LeafN                        = 2,
        LeafN_0                      = 2,
        leaf_reflectance             = 0.2,
        leaf_transmittance           = 0.2,
        lnb0                         = -5,
        lnb1                         = 18,
        lnfun                        = 0,
        longitude                    = -88,
        minimum_gbw                  = 0.08,
        mrc1                         = 0.02,
        mrc2                         = 0.03,
        net_assimilation_rate_shell  = 0.0,
        nlayers                      = 10,
        O2                           = 210,
        par_energy_content           = 0.219,
        par_energy_fraction          = 0.5,
        phi1                         = 0.01,
        phi2                         = 2,
        Rd                           = 1.1,
        remobilization_fraction      = 0.6,
        retrans                      = 0.9,
        retrans_rhizome              = 1.0,
        rfl                          = 0.2,
        rsdf                         = 0.44,
        rsec                         = 0.2,
        seneLeaf                     = 1600,
        seneRhizome                  = 5500,
        seneRoot                     = 5500,
        seneStem                     = 5500,
        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,
        Tfrosthigh                   = 5,
        Tfrostlow                    = 0,
        theta                        = 0.7,
        timestep                     = 1,
        tp1                          = 250,
        tp2                          = 350,
        tp3                          = 900,
        tp4                          = 1200,
        tp5                          = 3939,
        tpu_rate_max                 = 23,
        vmax1                        = 100,
        vmax_n_intercept             = 0,
        windspeed_height             = 5,
        wsFun                        = 2
    )
)