Biosphere

Submodules

There are two possible implementations of biosphere models:

• Ags
  • AgsState
    • AgsState.rs
    • AgsState.wl
    • AgsState.cliq
    • AgsState.wCO2
    • AgsState.cveg
    • AgsState.rsCO2
    • AgsState.gcco2
    • AgsState.ci
    • AgsState.co2abs
    • AgsState.wCO2A
    • AgsState.wCO2R
    • AgsState.wltend
  • AgsModel
    • AgsModel.init_state()
    • AgsModel.run()
    • AgsModel.compute_co2comp()
    • AgsModel.compute_gm()
    • AgsModel.compute_fmin()
    • AgsModel.compute_ds()
    • AgsModel.compute_d0()
    • AgsModel.compute_internal_co2()
    • AgsModel.compute_max_gross_primary_production()
    • AgsModel.compute_soil_moisture_stress_factor()
    • AgsModel.compute_gross_assimilation()
    • AgsModel.compute_dark_respiration()
    • AgsModel.compute_absorbed_par()
    • AgsModel.compute_canopy_co2_conductance()
    • AgsModel.compute_rs()
    • AgsModel.compute_light_use_efficiency()
    • AgsModel.compute_surface_co2_resistance()
    • AgsModel.compute_net_assimilation()
    • AgsModel.compute_soil_water_fraction()
    • AgsModel.compute_respiration()
    • AgsModel.scale_flux_to_mol()
    • AgsModel.compute_cliq()
    • AgsModel.compute_wltend()
    • AgsModel.run_tends()
    • AgsModel.integrate()
• Jarvis Stewart
  • JarvisStewartState
    • JarvisStewartState.rs
    • JarvisStewartState.wl
    • JarvisStewartState.cliq
    • JarvisStewartState.wCO2
    • JarvisStewartState.cveg
    • JarvisStewartState.wltend
  • JarvisStewartModel
    • JarvisStewartModel.init_state()
    • JarvisStewartModel.run()
    • JarvisStewartModel.compute_f1()
    • JarvisStewartModel.compute_f2()
    • JarvisStewartModel.compute_f3()
    • JarvisStewartModel.compute_f4()
    • JarvisStewartModel.compute_cliq()
    • JarvisStewartModel.compute_wltend()
    • JarvisStewartModel.run_tends()
    • JarvisStewartModel.integrate()

Module contents

class abcmodel.land.biosphere.JarvisStewartModel(rsmin=110.0, lai=2.0, gD=0.0, cveg=0.85, wmax=0.0002, wwilt=0.171, wfc=0.323, w2=0.21)

Bases: AbstractBiosphereModel[JarvisStewartState]

Jarvis-Stewart biosphere model with empirical surface resistance.

Parameters:

• rsmin (float) – minimum stomatal resistance [s m-1]. Default is 110.0.

• lai (float) – leaf area index [m2 m-2]. Default is 2.0.

• gD (float) – canopy rad extinction coefficient [-]. Default is 0.0.

• wmax (float) – maximum water storage capacity of the canopy [m]. Default is 0.0002.

• wwilt (float) – soil moisture content at wilting point [m3 m-3]. Default is 0.171.

• wfc (float) – soil moisture content at field capacity [m3 m-3]. Default is 0.323.

• w2 (float) – soil moisture content at the second layer [m3 m-3]. Default is 0.21.

init_state(rs=1000000.0, wl=0.0, cliq=0.0, wCO2=0.0)

Initialize the biosphere state.

Parameters:

• rs (float) – Surface resistance [s m-1]. Default is 1.0e6.

• wl (float) – Canopy water content [m]. Default is 0.0.

• cliq (float) – Wet fraction of canopy [-]. Default is 0.0.

• wCO2 (float) – Kinematic CO2 flux [mol m-2 s-1]. Default is 0.0.

• cveg – vegetation fraction [-]. Default is 0.85.

Returns:

The initialized JarvisStewartState.

run(state)

Compute biosphere surface resistance and canopy wet fraction.

compute_f1(in_srad)

Compute rad factor f1.

compute_f2(wg)

Compute soil moisture factor f2.

compute_f3(esat, e)

Compute VPD factor f3.

compute_f4(theta)

Compute temperature factor f4.

compute_cliq(wl)

Compute wet fraction of canopy cliq.

compute_wltend(le_liq)

Compute canopy water storage tendency.

run_tends(state, surf_state)

Compute biosphere tendencies that depend on surface fluxes.

integrate(state, dt)

Integrate canopy water content forward in time.

class abcmodel.land.biosphere.JarvisStewartState(rs, wl, cliq, wCO2, cveg, wltend=<factory>)

Bases: AbstractBiosphereState

Jarvis-Stewart biosphere state.

rs: Array

Surface resistance [s m-1].

wl: Array

Canopy water content [m].

cliq: Array

Wet fraction of canopy [-].

wCO2: Array

Kinematic CO2 flux [mol m-2 s-1].

cveg: Array

Vegetation fraction [-].

wltend: Array

Canopy water content tendency [m].

class abcmodel.land.biosphere.AgsModel(c3c4='c3', lai=2.0, cveg=0.85, wmax=0.0002, wwilt=0.171, wfc=0.323, w2=0.21)

Bases: AbstractBiosphereModel[AgsState]

Ags land surface biosphere model with coupled photosynthesis and stomatal conductance.

Parameters:

• c3c4 (str) – string indicating whether the model should use C3 or C4 photosynthesis. Default is “c3”.

• lai (float) – leaf area index [m2 m-2]. Default is 2.0.

• cveg (float) – vegetation fraction [-]. Default is 0.85.

• wmax (float) – maximum water storage capacity of the canopy [m]. Default is 0.0002.

• wwilt (float) – soil moisture content at wilting point [m3 m-3]. Default is 0.171.

• wfc (float) – soil moisture content at field capacity [m3 m-3]. Default is 0.323.

• w2 (float) – soil moisture content at the second layer [m3 m-3]. Default is 0.21.

init_state(rs=1000000.0, wl=0.0, cliq=0.0, wCO2=0.0)

Initialize the Ags state.

Parameters:

• rs (float) – Surface resistance [s m-1]. Default is 1.0e6.

• wl (float) – Canopy water content [m]. Default is 0.0.

• cliq (float) – Wet fraction of canopy [-]. Default is 0.0.

• wCO2 (float) – Total CO2 flux [mol m-2 s-1]. Default is 0.0.

Returns:

The initialized AgsState.

run(state)

Compute stomatal resistance and CO2 fluxes.

compute_co2comp(thetasurf)

Compute the CO₂ compensation concentration.

compute_gm(thetasurf)

Compute the mesophyll conductance.

compute_fmin(gm)

Compute minimum stomatal conductance factor.

compute_ds(surf_temp, e)

Compute vapor pressure deficit (ds) in kPa.

compute_d0(fmin)

Compute reference vapor pressure deficit.

compute_internal_co2(ds, d0, fmin, co2, co2comp)

Compute cfrac, co2abs, and ci (internal CO2 concentration).

compute_max_gross_primary_production(thetasurf)

Compute maximal gross primary production.

compute_soil_moisture_stress_factor(w2)

Compute effect of soil moisture stress.

compute_gross_assimilation(ammax, gm, ci, co2comp)

Compute gross assimilation rate.

compute_dark_respiration(am)

Compute dark respiration.

compute_absorbed_par(in_srad)

Compute absorbed photosynthetically active rad.

compute_canopy_co2_conductance(alphac, par, am, rdark, fstr, co2abs, co2comp, ds, d0, fmin)

Compute CO2 conductance at canopy level.

compute_rs(gcco2)

Compute surface resistance.

compute_light_use_efficiency(co2abs, co2comp)

Compute light use efficiency.

compute_surface_co2_resistance(gcco2)

Compute surface resistance to CO₂.

compute_net_assimilation(co2abs, ci, ra, rsCO2)

Compute net CO₂ assimilation rate.

compute_soil_water_fraction(wg)

Compute soil water fraction.

compute_respiration(temp_soil, fw)

Compute soil respiration.

scale_flux_to_mol(flux)

Scale a flux to mol m⁻² s⁻¹.

compute_cliq(wl)

Compute wet fraction of canopy.

compute_wltend(le_liq)

Compute canopy water storage tendency.

run_tends(state, surf_state)

Compute biosphere tendencies that depend on surface fluxes.

integrate(state, dt)

Integrate canopy water content forward in time.

class abcmodel.land.biosphere.AgsState(rs, wl, cliq, wCO2, cveg, rsCO2=<factory>, gcco2=<factory>, ci=<factory>, co2abs=<factory>, wCO2A=<factory>, wCO2R=<factory>, wltend=<factory>)

Bases: AbstractBiosphereState

A-gs biosphere state.

rs: Array

Surface resistance [s m-1].

wl: Array

Canopy water content [m].

cliq: Array

Wet fraction of canopy [-].

wCO2: Array

Total CO2 flux [mol m-2 s-1].

cveg: Array

Vegetation fraction [-].

rsCO2: Array

Stomatal resistance to CO2.

gcco2: Array

Conductance to CO2.

ci: Array

Intercellular CO2 concentration.

co2abs: Array

CO2 assimilation rate / concentration.

wCO2A: Array

Net assimilation flux [mol m-2 s-1].

wCO2R: Array

Respiration flux [mol m-2 s-1].

wltend: Array

Canopy water content tendency [m].