Abiotic model configuration#

Configuration for the abiotic model includes three sections:

  • An expanded set of constants values ([abiotic.constants]).

  • A set of upper and lower bounds on the predicted microclimate variables ([abiotic.bounds]). This uses the same defaults as the simple abiotic model.

  • The abiotic model uses the simple abiotic model to initialise the system state and also requires the simple constants used by that model ([abiotic.simple_constants]).

The last two sections are defined identically to the abiotic simple above and so follow the structure for the bounds and simple constants. The only difference is that the should use the section names for the abiotic model.

Abiotic constants#

[abiotic.constants]
leaf_emissivity = 0.98
soil_emissivity = 0.95
leaf_albedo = 0.15
bulk_density_soil = 1175.0
wind_reference_height = 10.0
latent_heat_vap_equ_factors = [
    1918460.0,
    33.91,
]
zero_plane_scaling_parameter = 7.5
substrate_surface_roughness_length = 0.003
roughness_element_drag_coefficient = 0.3
roughness_sublayer_depth_parameter = 0.193
max_ratio_wind_to_friction_velocity = 0.3
min_windspeed_below_canopy = 0.1
min_roughness_length = 0.01
soil_thermal_conductivity = 1.206
specific_heat_capacity_soil = 881.0
surface_albedo = 0.125
saturated_pressure_slope_parameters = [
    4098.0,
    0.6108,
    17.27,
    237.3,
]
dry_air_factor = 0.378
initial_flux_value = 0.001
aerodynamic_resistance_canopy_night = 50.0
aerodynamic_resistance_soil_night = 50.0
aerodynamic_resistance_canopy_day = 20.0
max_mixing_coefficient = 1.0
fraction_par_used_for_photosynthesis = 0.5
leaf_absorptance_non_par = 0.5
par_fraction_of_shortwave_radiation = 0.46
maxiter_secant_solver = 8
convergence_tolerance_secant_solver = 0.01
small_perturbation_second_guess_secant_solver = 1e-06
denominator_tolerance = 1e-12
min_specific_humidity = 0.001
understorey_ventilation_rate = 0.1
extinction_coefficient_longwave = 0.5
minimum_mixing_depth = 1.5
min_leaf_area_index_for_mixing = 0.5
abiotic.constants.leaf_emissivity

Leaf emissivity, unitless.

Leaf emissivity is a measure of how efficiently a leaf emits thermal radiation compared to a perfect blackbody, typically ranging from 0.95 to 0.99. Value for tropical vegetation is taken from Ma et al. (2019). Default = 0.98

abiotic.constants.soil_emissivity

Soil emissivity, dimensionless.

Soil emissivity is a measure of how efficiently the soil surface emits thermal radiation compared to a perfect blackbody, with values typically ranging from 0.90 to 0.98 depending on soil texture, moisture, and surface roughness. Value taken from Mölders (2005). Default = 0.95

abiotic.constants.leaf_albedo

Leaf albedo, unitless.

Leaf albedo is the fraction of incoming solar radiation that a leaf reflects, typically ranging from 0.12 to 0.18 in tropical forests due to their dark, broadleaf surfaces. Value here is taken from Su et al. (2021). Default = 0.15

abiotic.constants.bulk_density_soil

Bulk density of soil, [kg m-3].

Bulk density describes the mass of dry soil per unit volume, including both the solid soil particles and the pore spaces between them. Value for average rainforest soil is taken from Gupta et al. (2021). Default = 1175.0

abiotic.constants.wind_reference_height

Reference height for wind speed above the canopy, [m].

The reference height for horizontal wind is typically 10m above ground compared to 2m for other atmospheric variables such as temperature and relative humidity. We assume here that the reference height is above the canopy, please check the input data carefully and be aware of limitations. Default = 10.0

abiotic.constants.latent_heat_vap_equ_factors

Factors in calculation of latent heat of vapourisation.

Implementation after Maclean and Klinges (2021), value is taken from Henderson-Sellers (1984). Default = (1918460.0, 33.91)

abiotic.constants.zero_plane_scaling_parameter

Control parameter for scaling zero displacement to height, dimensionless.

Implementation after Maclean and Klinges (2021), value is taken from Raupach (1994). Default = 7.5

abiotic.constants.substrate_surface_roughness_length

Substrate-surface roughness length, m.

The substrate-surface roughness length is the “baseline roughness” of the ground itself before adding vegetation on top. Implementation and value from Maclean and Klinges (2021). Default = 0.003

abiotic.constants.roughness_element_drag_coefficient

Roughness-element drag coefficient, dimensionless.

The roughness-element drag coefficient refers to the dimensionless coefficient used to quantify the drag force exerted by individual roughness elements (such as buildings, trees, or surface irregularities) on airflow, influencing the overall aerodynamic characteristics of a surface within the atmospheric boundary layer. Implementation and value from Maclean and Klinges (2021). Default = 0.3

abiotic.constants.roughness_sublayer_depth_parameter

Parameter characterizes the roughness sublayer depth.

The roughness sublayer depth refers to the layer near the surface where the effects of surface roughness significantly influence airflow, turbulence, momentum transfer, typically extending up to about 10% of the height of the roughness elements or features on the surface. This layer is characterized by intense turbulence and rapid velocity changes due to surface irregularities. Implementation and value taken from (Maclean and Klinges, 2021). Default = 0.193

abiotic.constants.max_ratio_wind_to_friction_velocity

Maximum ratio of wind velocity to friction velocity, dimensionless.

The maximum ratio of wind velocity to friction velocity refers to the highest observed or theoretical value of the ratio between the wind speed at a given height and the surface friction velocity (u*), indicating the efficiency of momentum transfer from the atmosphere to the surface. Implementation and value from Maclean and Klinges (2021). Default = 0.3

abiotic.constants.min_windspeed_below_canopy

Minimum wind speed below the canopy or in absence of vegetation, [m s-1]. Default = 0.1

abiotic.constants.min_roughness_length

Minimum roughness length, [m].

The minimum roughness length represents the lowest height at which the surface roughness significantly affects the wind flow over a particular terrain or surface. Implementation and value from Maclean and Klinges (2021). Default = 0.01

abiotic.constants.soil_thermal_conductivity

Soil thermal conductivity, [W m-1 K-1].

Soil thermal conductivity is a measure of the soil’s ability to conduct heat, influenced by factors such as moisture content, texture, and density. Value is taken from Rasimeng (2020). Default = 1.206

abiotic.constants.specific_heat_capacity_soil

Specific heat capacity of soil, [J kg-1 K-1].

Specific heat capacity of soil is the amount of heat required to raise the temperature of a unit mass of soil by one degree Celsius (or Kelvin), and depends on soil composition, moisture content, and organic matter. Value taken from Mölders (2005). Default = 881

abiotic.constants.surface_albedo

Mean surface albedo of a tropical rainforest in South East Asia, dimensionless.

The value is takes from a study that compares changes in surface albedo before and after deforestation in South East Asia (Wilson, 2020). Default = 0.125

abiotic.constants.saturated_pressure_slope_parameters

List of parameters to calculate the slope of saturated vapour pressure curve. Default = (4098.0, 0.6108, 17.27, 237.3)

abiotic.constants.dry_air_factor

Dry air factor, dimensionless.

This term accounts for the proportion of dry air when computing the partitioning of total air pressure. It is the complement of the molecular_weight_ratio_water_to_dry_air in core.constants. Default = 0.378

abiotic.constants.initial_flux_value

Initial non-zero fill value for energy fluxes, [W m-2]. Default = 0.001

abiotic.constants.aerodynamic_resistance_canopy_night

Aerodynamic resistance of the canopy at night, [s m-1]. Default = 50.0

abiotic.constants.aerodynamic_resistance_soil_night

Aerodynamic resistance of the soil at night, [s m-1]. Default = 50.0

abiotic.constants.aerodynamic_resistance_canopy_day

Aerodynamic resistance of the canopy during the day, [s m-1]. Default = 20.0

abiotic.constants.max_mixing_coefficient

Maximum turbulent mixing coefficients, [m2 s-1]. Default = 1.0

abiotic.constants.fraction_par_used_for_photosynthesis

Fraction of photosynthetically active radiation used for photosynthesis, dimensionless. Default = 0.5

abiotic.constants.leaf_absorptance_non_par

Leaf absorptance for non-photosynthetically active radiation, dimensionless. Default = 0.5

abiotic.constants.par_fraction_of_shortwave_radiation

Fraction of shortwave radiation that is photosynthetically active, dimensionless.

Value is taken from the P-Model:

Convert from downward shortwave radiation [W m-2] to photosynthetic photon flux density (PPFD)[µmol m-2 s-1]. 1 W m-2 of sunlight is roughly 4.57 µmol m-2 s-1 of full spectrum sunlight, of which about 4.57 * 46% = 2.04 µmol m-2 s-1 is PPFD. Default = 0.46

abiotic.constants.maxiter_secant_solver

Maximum number of secant iterations to solve for canopy temperature. Default = 8

abiotic.constants.convergence_tolerance_secant_solver

Convergence tolerance for secant solver, in max absolute update. Default = 0.01

abiotic.constants.small_perturbation_second_guess_secant_solver

Small perturbation for second initial guess in secant solver. Default = 1e-06

abiotic.constants.denominator_tolerance

Small value to prevent division by zero. Default = 1e-12

abiotic.constants.min_specific_humidity

Minimum value for specific humidity to avoid dividion by zero, [kg kg-1]. Default = 0.001

abiotic.constants.understorey_ventilation_rate

Understorey ventilation rate, comes into place when there is no canopy, [s-1]. Default = 0.1

abiotic.constants.extinction_coefficient_longwave

Extinction coefficient for longwave radiation, dimensionless. Default = 0.5

abiotic.constants.minimum_mixing_depth

Minimum mixing depth for lowest canopy layer, [m].

This is to prevent unrealistically low mixing depths and therefore high temperatures in the lowest canopy layer when the layer height is very low. Note that this is an artificial inflation of the mixing depth. Default = 1.5

abiotic.constants.min_leaf_area_index_for_mixing

Minimum leaf area index required for turbulent mixing to occur, [m m-1]. Default = 0.5

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