API documentation for the constants module
The models.soil.constants module contains a set of dataclasses containing
constants (fitting relationships taken from the literature) required by the broader
soil module
Classes:
|
Dataclass to store all constants for the soil model. |
- class virtual_ecosystem.models.soil.constants.SoilConsts(reference_cue: float = 0.6, cue_reference_temp: float = 15.0, cue_with_temperature: float = 0.012, soil_microbe_water_potential_optimum: float = -3.0, soil_microbe_water_potential_halt: float = -15800.0, microbial_water_response_curvature: float = 1.47, arrhenius_reference_temp: float = 12.0, max_uptake_rate_labile_C: float = 0.04, activation_energy_microbial_uptake: float = 47000, half_sat_labile_C_uptake: float = 0.364, activation_energy_labile_C_saturation: float = 30000, half_sat_pom_decomposition: float = 70.0, activation_energy_pom_decomp_saturation: float = 30000, max_decomp_rate_pom: float = 60.0, activation_energy_pom_decomp_rate: float = 37000, half_sat_maom_decomposition: float = 350.0, activation_energy_maom_decomp_saturation: float = 30000, max_decomp_rate_maom: float = 24.0, activation_energy_maom_decomp_rate: float = 47000, microbial_turnover_rate: float = 0.005, pom_enzyme_turnover_rate: float = 0.024, maom_enzyme_turnover_rate: float = 0.024, maintenance_pom_enzyme: float = 0.01, maintenance_maom_enzyme: float = 0.01, necromass_to_lmwc: float = 0.25, min_pH_microbes: float = 2.5, lowest_optimal_pH_microbes: float = 4.5, highest_optimal_pH_microbes: float = 7.5, max_pH_microbes: float = 11.0, base_soil_protection: float = 0.694, soil_protection_with_clay: float = 1.36, clay_necromass_decay_exponent: float = -0.8, pom_decomposition_fraction_lmwc: float = 0.5, solubility_coefficient_lmwc: float = 0.05)
Dataclass to store all constants for the soil model.
Attributes:
Activation energy for labile C uptake saturation constant [J K^-1].
Activation energy for decomposition of mineral associated organic matter.
Activation energy for MAOM decomposition saturation constant [J K^-1].
Activation energy for microbial maintenance turnover rate [J K^-1].
Activation energy for microbial uptake of low molecular weight carbon [J K^-1].
Activation energy for decomposition of particulate organic matter [J K^-1].
Activation energy for POM decomposition saturation constant [J K^-1].
Reference temperature for the Arrhenius equation [C].
Basal change in saturation constants due to soil structure [unitless]
Change in proportion of necromass which decays with increasing soil clay content.
Reference temperature for carbon use efficiency [degrees C].
Change in carbon use efficiency with increasing temperature [degree C^-1].
Half saturation constant for microbial uptake of labile carbon (LMWC).
Half saturation constant for MAOM decomposition to LMWC [kg C m^-3].
Half saturation constant for POM decomposition to LMWC [kg C m^-3].
Soil pH below which microbial activity is not inhibited at all [unitless].
Soil pH above which microbial activity is not inhibited at all [unitless].
Fraction of maintenance synthesis used to produce MAOM degrading enzymes.
Fraction of maintenance synthesis used to produce POM degrading enzymes.
Turnover rate for MAOM degrading enzymes [day^-1].
Maximum rate for mineral associated organic matter decomposition enzyme.
Maximum rate for particulate organic matter break down (at reference temp).
Soil pH above which microbial activity is completely inhibited [unitless].
Maximum rate at the reference temperature of labile carbon uptake [day^-1].
Microbial turnover rate at reference temperature [day^-1].
Curvature of function for response of soil microbial rates to water potential.
Soil pH below which microbial activity is completely inhibited [unitless].
Proportion of necromass that flows to LMWC rather than POM [unitless].
Fraction of decomposed POM that becomes LMWC rather than MAOM [unitless].
Turnover rate for POM degrading enzymes [day^-1].
Carbon use efficiency of community at the reference temperature [no units].
The water potential at which soil microbial activity stops entirely [kPa].
The water potential at which soil microbial rates are maximised [kPa].
Rate at which soil protection of carbon increases with clay content [unitless].
Solubility coefficient for low molecular weight organic carbon [unitless].
- activation_energy_labile_C_saturation: float = 30000
Activation energy for labile C uptake saturation constant [J K^-1].
Taken from Wang et al. (2013).
- activation_energy_maom_decomp_rate: float = 47000
Activation energy for decomposition of mineral associated organic matter.
Units of [J K^-1]. Taken from Wang et al. (2013).
- activation_energy_maom_decomp_saturation: float = 30000
Activation energy for MAOM decomposition saturation constant [J K^-1].
Taken from Wang et al. (2013).
- activation_energy_microbial_turnover = 20000
Activation energy for microbial maintenance turnover rate [J K^-1].
Value taken from Wang et al. (2013). The microbial turnover rate that this activation energy corresponds to is given by
microbial_turnover_rate.
- activation_energy_microbial_uptake: float = 47000
Activation energy for microbial uptake of low molecular weight carbon [J K^-1].
Value taken from Wang et al. (2013). The maximum labile carbon uptake rate that this activation energy corresponds to is given by
max_uptake_rate_labile_C.
- activation_energy_pom_decomp_rate: float = 37000
Activation energy for decomposition of particulate organic matter [J K^-1].
Taken from Wang et al. (2013).
- activation_energy_pom_decomp_saturation: float = 30000
Activation energy for POM decomposition saturation constant [J K^-1].
Taken from Wang et al. (2013).
- arrhenius_reference_temp: float = 12.0
Reference temperature for the Arrhenius equation [C].
This is the reference temperature used in Wang et al. (2013), which is the source of the activation energies and corresponding rates.
- base_soil_protection: float = 0.694
Basal change in saturation constants due to soil structure [unitless]
This value is multiplicative and is taken from Fatichi et al. (2019).
- clay_necromass_decay_exponent: float = -0.8
Change in proportion of necromass which decays with increasing soil clay content.
[unitless]. The function this is used in is an exponential, and the sign should be negative so increases in clay leads to a lower proportion of necromass decaying to LMWC. The value of this constant is taken from Fatichi et al. (2019).
- cue_reference_temp: float = 15.0
Reference temperature for carbon use efficiency [degrees C].
Default value taken from Abramoff et al. (2018).
- cue_with_temperature: float = 0.012
Change in carbon use efficiency with increasing temperature [degree C^-1].
Default value taken from Abramoff et al. (2018).
- half_sat_labile_C_uptake: float = 0.364
Half saturation constant for microbial uptake of labile carbon (LMWC).
[kg C m^-3]. This was calculated from the value provided in Wang et al. (2013) assuming an average bulk density of 1400 [kg m^-3]. The reference temperature is given by
arrhenius_reference_temp, and the corresponding activation energy is given byactivation_energy_labile_C_saturation.
- half_sat_maom_decomposition: float = 350.0
Half saturation constant for MAOM decomposition to LMWC [kg C m^-3].
This was calculated from the value provided in Wang et al. (2013) assuming an average bulk density of 1400 [kg m^-3]. The reference temperature is given by
arrhenius_reference_temp, and the corresponding activation energy is given byactivation_energy_maom_decomp_saturation.
- half_sat_pom_decomposition: float = 70.0
Half saturation constant for POM decomposition to LMWC [kg C m^-3].
This was calculated from the value provided in Wang et al. (2013) assuming an average bulk density of 1400 [kg m^-3]. The reference temperature is given by
arrhenius_reference_temp, and the corresponding activation energy is given byactivation_energy_pom_decomp_saturation.
- highest_optimal_pH_microbes: float = 7.5
Soil pH below which microbial activity is not inhibited at all [unitless].
This value cannot be smaller than
lowest_optimal_pH_microbesor larger thanmax_pH_microbes. The default value was obtained by averaging the fungi and bacteria specific values given in Orwin et al. (2011).
- lowest_optimal_pH_microbes: float = 4.5
Soil pH above which microbial activity is not inhibited at all [unitless].
This value cannot be smaller than
min_pH_microbesor larger thanhighest_optimal_pH_microbes. The default value was obtained by averaging the fungi and bacteria specific values given in Orwin et al. (2011).
- maintenance_maom_enzyme: float = 0.01
Fraction of maintenance synthesis used to produce MAOM degrading enzymes.
[unitless]. Value taken from Wang et al. (2013).
- maintenance_pom_enzyme: float = 0.01
Fraction of maintenance synthesis used to produce POM degrading enzymes.
[unitless]. Value taken from Wang et al. (2013).
- maom_enzyme_turnover_rate: float = 0.024
Turnover rate for MAOM degrading enzymes [day^-1].
Value taken from Wang et al. (2013).
- max_decomp_rate_maom: float = 24.0
Maximum rate for mineral associated organic matter decomposition enzyme.
Units of [day^-1]. The rate is for a reference temperature which is given by
arrhenius_reference_temp, and the corresponding activation energy is given byactivation_energy_maom_decomp_rate. The value is taken from Wang et al. (2013).
- max_decomp_rate_pom: float = 60.0
Maximum rate for particulate organic matter break down (at reference temp).
Units of [day^-1]. The reference temperature is given by
arrhenius_reference_temp, and the corresponding activation energy is given byactivation_energy_pom_decomp_rate.TODO - Source of this constant is not completely clear, investigate this further once lignin chemistry is added.
- max_pH_microbes: float = 11.0
Soil pH above which microbial activity is completely inhibited [unitless].
This value cannot be smaller than
highest_optimal_pH_microbes. The default value was obtained by averaging the fungi and bacteria specific values given in Orwin et al. (2011).
- max_uptake_rate_labile_C: float = 0.04
Maximum rate at the reference temperature of labile carbon uptake [day^-1].
The reference temperature is given by
arrhenius_reference_temp, and the corresponding activation energy is given byactivation_energy_microbial_uptake.TODO - Source of this constant is not completely clear, investigate this further once fungi are added.
- microbial_turnover_rate: float = 0.005
Microbial turnover rate at reference temperature [day^-1].
The reference temperature is given by
arrhenius_reference_temp, and the corresponding activation energy is given byactivation_energy_microbial_turnover.TODO - Source of this constant is not completely clear, investigate this further once fungi are added.
- microbial_water_response_curvature: float = 1.47
Curvature of function for response of soil microbial rates to water potential.
[unitless]. Value is taken from :cite:t`moyano_responses_2013`.
- min_pH_microbes: float = 2.5
Soil pH below which microbial activity is completely inhibited [unitless].
This value cannot be larger than
lowest_optimal_pH_microbes. The default value was obtained by averaging the fungi and bacteria specific values given in Orwin et al. (2011).
- necromass_to_lmwc: float = 0.25
Proportion of necromass that flows to LMWC rather than POM [unitless].
Value taken from Wang et al. (2013).
- pom_decomposition_fraction_lmwc: float = 0.5
Fraction of decomposed POM that becomes LMWC rather than MAOM [unitless].
Value taken from Wang et al. (2013).
- pom_enzyme_turnover_rate: float = 0.024
Turnover rate for POM degrading enzymes [day^-1].
Value taken from Wang et al. (2013).
- reference_cue: float = 0.6
Carbon use efficiency of community at the reference temperature [no units].
Default value taken from Abramoff et al. (2018).
- soil_microbe_water_potential_halt: float = -15800.0
The water potential at which soil microbial activity stops entirely [kPa].
Value is taken from :cite:t`moyano_responses_2013`.
- soil_microbe_water_potential_optimum: float = -3.0
The water potential at which soil microbial rates are maximised [kPa].
Value is taken from :cite:t`moyano_responses_2013`.