Virtual Ecosystem array variables#

The table below list all of the variables that are stored centrally within Virtual Ecosystem simulations. These variables are arrays of data that are structured using the core axes of the simulation.

Each science model declares which of these variables are used when the model runs. There are five different usage cases, identifying sets of variables that are:

  • required to setup a model,

  • populated when the model is set up,

  • required when the model updates,

  • populated when the model first updates, and

  • updated by the model at every time step.

The variables required to set up a model can be further split into two classes:

  • Input variables: these are the variables that you will need to provide through the model data configuration for a simulation. These variables are shown in bold in the table below.

  • Calculated variables: these variables are calculated from the input variables by the setup process of another model.

Filter variables
Name Name Units Axes Description Variable Type Req. Init Pop. Init Req. Update Pop. Update Updated
population_densities individual m-2 Density of animal populations. float animal
air_heat_conductivity mol m-2 s-1 spatial Air heat conductivity between layers float
air_temperature C spatial Air temperature profile float soil abiotic,abiotic_simple animal,hydrology,litter,plants,soil abiotic,abiotic_simple
air_temperature_ref C spatial,time Air temperature at reference height (2m) float abiotic,abiotic_simple,hydrology abiotic,abiotic_simple
diurnal_temperature_range C spatial Diurnal air temperature range float abiotic,abiotic_simple animal abiotic
total_animal_respiration ppm spatial Animal respiration aggregated over all functional types float animal animal
atmospheric_co2 ppm spatial Atmospheric CO2 concentration profile float abiotic,abiotic_simple plants abiotic_simple
atmospheric_co2_ref ppm spatial,time Atmospheric CO2 concentration at reference height (above canopy) float abiotic,abiotic_simple abiotic,abiotic_simple
atmospheric_pressure kPa spatial Atmospheric pressure profile float abiotic,abiotic_simple hydrology,plants abiotic_simple
atmospheric_pressure_ref kPa spatial,time Atmospheric pressure at reference height (2m) float abiotic,abiotic_simple,hydrology abiotic,abiotic_simple
attenuation_coefficient - spatial Wind attenuation coefficient float
baseflow mm spatial Baseflow float hydrology hydrology
bypass_flow mm spatial Bypass flow float hydrology hydrology
shortwave_absorption W m-2 spatial Shortwave radiation absorbed by individual canopy layers float abiotic,abiotic_simple plants abiotic,abiotic_simple plants
canopy_height m spatial Canopy height float
canopy_temperature C spatial Canopy temperature of individual layers float abiotic,abiotic_simple animal abiotic
conductivity_from_ref_height mol m-2 s-1 spatial Conductivity from reference height float
conductivity_from_soil mol m-2 s-1 spatial Conductivity from soil float
condensation mm spatial Condensated water from supersaturation in the atmosphere float abiotic hydrology abiotic,hydrology abiotic
diabatic_correction_heat_above - spatial Diabatic correction factor for heat above canopy float
diabatic_correction_heat_canopy - spatial Diabatic correction factor for heat in canopy float
diabatic_correction_momentum_above - spatial Diabatic correction factor for momentum above canopy float
diabatic_correction_momentum_canopy - spatial Diabatic correction factor for momentum in canopy float
elevation m spatial Elevation above sea level float hydrology
transpiration mm spatial Transpiration from the canopy and subcanopy float abiotic,hydrology plants plants
friction_velocity m s-1 spatial Friction velocity float
ground_heat_flux W m-2 spatial Ground heat flux float abiotic abiotic
conductive_flux_understorey W m-2 spatial Conductive flux between soil and understorey float
groundwater_storage mm spatial Groundwater Storage float hydrology hydrology
latent_heat_flux W m-2 spatial Latent heat flux profile float abiotic abiotic
latent_heat_flux_soil W m-2 spatial Latent heat flux from topsoil layer float
latent_heat_vapourisation kJ kg-1 spatial Latent heat of vapourisation float abiotic hydrology abiotic
layer_heights m spatial Heights of model layers float abiotic,abiotic_simple,hydrology plants abiotic,abiotic_simple,hydrology plants
interception mm spatial Intercepted rainfall in canopy float hydrology hydrology
leaf_air_heat_conductivity mol m-2 s-1 spatial Leaf air heat conductivity float
leaf_area_index m m-1 spatial Leaf area index float abiotic,abiotic_simple plants abiotic,abiotic_simple,hydrology plants
leaf_vapour_conductivity mol m-2 s-1 spatial Leaf vapour conductivity float
longwave_canopy W m-2 spatial Longwave emission from individual canopy layers float
longwave_emission_soil W m-2 spatial Longwave emission from topsoil layer float
longwave_emission W m-2 spatial Longwave emission float abiotic abiotic
matric_potential kPa spatial Matric potential float soil hydrology litter,soil hydrology
mean_annual_temperature C spatial,time Mean annual temperature = temperature of deepest soil layer float abiotic,abiotic_simple abiotic_simple
mean_mixing_length m spatial Mean mixing length float
mixing_coefficient s-1 spatial Turbulent mixing coefficient float
ventilation_rate s-1 spatial ventilation rate between top of canopy and atmosphere above float
net_radiation W m-2 spatial Net radiation float abiotic,abiotic_simple hydrology abiotic,abiotic_simple
density_air kg m-3 spatial Temperature-dependent density of air float abiotic hydrology hydrology abiotic
plant_net_co2_assimilation ppm Plant net CO2 assimilation
downward_shortwave_radiation W m-2 spatial,time Top of canopy downward shortwave radiation (DSR) float plants abiotic,plants
downward_longwave_radiation W m-2 spatial,time Top of canopy downward longwave radiation (DLR) float abiotic abiotic
precipitation mm spatial,time Precipitation input at the top of the canopy float hydrology
precipitation_surface mm spatial Precipitation that reaches surface float hydrology hydrology
relative_humidity % spatial Relative humidity profile float abiotic,abiotic_simple hydrology abiotic,abiotic_simple
relative_humidity_ref % spatial,time Relative humidity at reference height (2m) float abiotic,abiotic_simple abiotic,abiotic_simple
relative_turbulence_intensity - spatial Relative turbulence intensity float
river_discharge_rate m3 s-1 spatial River discharge rate float hydrology hydrology
aerodynamic_resistance_soil s m-1 spatial Aerodynamic resistance soil float hydrology abiotic hydrology
aerodynamic_resistance_canopy s m-1 spatial Aerodynamic resistance canopy float abiotic hydrology hydrology abiotic
canopy_evaporation mm spatial Canopy evaporation float abiotic hydrology hydrology
roughness_length_momentum m spatial Roughness length for momentum float
saturated_vapour_pressure_ref kPa spatial,time Saturated vapour pressure at reference height (2m) float
sensible_heat_flux W m-2 spatial Sensible heat flux profile float abiotic abiotic
sensible_heat_flux_soil W m-2 spatial Sensible heat flux from topsoil layer float
shortwave_radiation_surface W m-2 spatial Shortwave radiation at the surface float
soil_absorption W m-2 spatial Shortwave radiation absorbed by topsoil layer float
soil_vapour_pressure kPa spatial Soil vapour pressure float
subsurface_runoff_routed_plus_local mm spatial Subsurface flow contributing to river discharge in each grid cell float hydrology hydrology
soil_evaporation mm spatial Soil evaporation float abiotic hydrology hydrology
soil_moisture mm spatial Soil moisture float hydrology hydrology,soil hydrology
soil_respiration ppm spatial Soil respiration
soil_temperature C spatial Soil temperature profile float soil abiotic,abiotic_simple animal,litter,soil abiotic,abiotic_simple
specific_heat_air J kg-1 K-1 spatial Specific heat of air float abiotic hydrology hydrology abiotic
specific_humidity g kg-1 spatial Specific humidity of air
stomatal_conductance mol m-2 s-1 spatial Stomatal conductance float hydrology abiotic,hydrology
stream_flow mm per time step spatial Estimated stream flow float
subsurface_flow mm spatial Subsurface flow float hydrology hydrology
surface_runoff mm spatial Surface runoff generated in each grid cell float hydrology hydrology
surface_runoff_routed_plus_local mm spatial Surface runoff contributing to river discharge in each grid cell float hydrology hydrology
topofcanopy_radiation W m-2 spatial Top of canopy downward shortwave radiation float
total_runoff mm spatial Total runoff through each grid cell float hydrology hydrology
vapour_pressure kPa spatial Vapour pressure profile float abiotic,abiotic_simple abiotic,abiotic_simple
vapour_pressure_ref kPa spatial,time Vapour pressure at reference height (2m) float abiotic,abiotic_simple
vapour_pressure_deficit kPa spatial Vapour pressure deficit profile float abiotic,abiotic_simple hydrology,plants abiotic,abiotic_simple
vapour_pressure_deficit_ref kPa spatial,time Vapour pressure deficit at reference height (2m) float abiotic,abiotic_simple abiotic,abiotic_simple
vertical_flow mm per time step (currently day) spatial Vertical flow of water through soil column float soil hydrology hydrology
wind_speed m s-1 spatial Wind profile within and below canopy float abiotic,abiotic_simple hydrology abiotic,abiotic_simple
wind_speed_ref m s-1 spatial,time Wind speed at reference height (10m) float abiotic,abiotic_simple abiotic,abiotic_simple
zero_plane_displacement m spatial Zero plane displacement height float
soil_cnp_pool_lmwc kg m^-3 spatial Soil low molecular weight organic pool. Carbon, nitrogen and phosphorous content float soil soil soil
soil_cnp_pool_maom kg m^-3 spatial Soil mineral associated organic matter pool. Carbon, nitrogen and phosphorous content float soil soil soil
soil_c_pool_bacteria kg{C} m^-3 spatial Soil bacterial biomass (carbon) pool float soil animal,soil soil
soil_c_pool_saprotrophic_fungi kg{C} m^-3 spatial Soil saprotrophic fungal biomass (carbon) pool float soil animal,soil soil
soil_c_pool_arbuscular_mycorrhiza kg{C} m^-3 spatial Soil arbuscular mycorrhizal fungal biomass (carbon) pool float soil animal,soil soil
soil_c_pool_ectomycorrhiza kg{C} m^-3 spatial Soil ectomycorrhizal fungal biomass (carbon) pool float soil animal,soil soil
soil_cnp_pool_pom kg m^-3 spatial Particulate organic matter pool. Carbon, nitrogen and phosphorous content float soil animal,soil soil
soil_cnp_pool_necromass kg m^-3 spatial Necrotic organic matter pool. Carbon, nitrogen and phosphorous content float soil soil soil
soil_n_pool_ammonium kg{N} m^-3 spatial Amount of nitrogen contained in the soil ammonium (NH4+) pool float soil soil soil
soil_n_pool_nitrate kg{N} m^-3 spatial Amount of nitrogen contained in the soil nitrate (NO3-) pool float soil soil soil
soil_p_pool_primary kg{P} m^-3 spatial Amount of phosphorus in a primary mineral form float soil soil soil
soil_p_pool_secondary kg{P} m^-3 spatial Amount of inorganic phosphorus that is associated with secondary minerals float soil soil soil
soil_p_pool_labile kg{P} m^-3 spatial Amount of inorganic phosphorus that is in a labile form float soil soil soil
pH pH spatial Soil pH values for each grid cell float soil soil
litter_pool_above_metabolic_cnp kg m^-2 spatial Above ground metabolic litter pool, carbon, nitrogen and phosphorus mass float animal,litter animal,litter litter
litter_pool_above_structural_cnp kg m^-2 spatial Above ground structural litter pool, carbon, nitrogen and phosphorus mass float animal,litter animal,litter litter
litter_pool_woody_cnp kg m^-2 spatial Woody litter pool, carbon, nitrogen and phosphorus mass float animal,litter animal,litter litter
litter_pool_below_metabolic_cnp kg m^-2 spatial Below ground metabolic litter pool, carbon, nitrogen and phosphorus mass float animal,litter animal,litter litter
litter_pool_below_structural_cnp kg m^-2 spatial Below ground structural litter pool, carbon, nitrogen and phosphorus mass float animal,litter animal,litter litter
litter_mineralisation_rate_cnp kg m^-3 day^-1 spatial Rate of carbon, nitrogen and phosphorus addition to soil from litter float soil litter litter
lignin_above_structural unitless spatial Proportion of above ground structural litter carbon which is lignin carbon float litter litter litter
lignin_below_structural unitless spatial Proportion of below ground structural litter carbon which is lignin carbon float litter litter litter
lignin_woody unitless spatial Proportion of dead wood carbon which is lignin carbon float litter litter litter
decomposed_excrement_cnp kg m^-2 day^-1 spatial Flow rates of carbon, nitrogen and phosphorous into the soil due to animal excrement decay float soil animal animal
decomposed_carcasses_cnp kg m^-2 day^-1 spatial Flow rates of carbon, nitrogen and phosphorous into the soil due to animal carcass decay float soil animal animal
herbivory_waste_leaf_cnp kg spatial Carbon, nitrogen and phosphorus mass of leaves added to the litter due to herbivore mechanical inefficiency float litter animal animal
herbivory_waste_leaf_lignin unitless spatial Proportion of leaf carbon added to litter due to herbivore mechanical inefficiency that is lignin carbon float litter animal animal
litter_consumed_above_metabolic_cnp kg spatial Amount of above-ground metabolic litter that has been consumed by animals, in carbon, nitrogen and phosphorus terms float animal litter animal
litter_consumed_above_structural_cnp kg spatial Amount of above-ground structural litter that has been consumed by animals, in carbon, nitrogen and phosphorus terms float animal litter animal
litter_consumed_woody_cnp kg spatial Amount of woody litter that has been consumed by animals, in carbon, nitrogen and phosphorus terms float animal litter animal
litter_consumed_below_metabolic_cnp kg spatial Amount of below-ground metabolic litter that has been consumed by animals, in carbon, nitrogen and phosphorus terms float animal litter animal
litter_consumed_below_structural_cnp kg spatial Amount of below-ground structural litter that has been consumed by animals, in carbon, nitrogen and phosphorus terms float animal litter animal
animal_pom_consumption_cnp kg m^-3 day^-1 spatial Rate at which carbon, nitrogen and phosphorus components of soil particulate organic matter are consumed by animals float soil animal animal
animal_bacteria_consumption kg C m^-3 day^-1 spatial Rate at which soil bacteria are being consumed by animals float soil animal animal
animal_saprotrophic_fungi_consumption kg C m^-3 day^-1 spatial Rate at which saprotrophic soil fungi are being consumed by animals float soil animal animal
animal_ectomycorrhiza_consumption kg C m^-3 day^-1 spatial Rate at which ectomycorrhizal soil fungi are being consumed by animals float soil animal animal
animal_arbuscular_mycorrhiza_consumption kg C m^-3 day^-1 spatial Rate at which arbuscular mycorrhizal soil fungi are being consumed by animals float soil animal animal
fungal_fruiting_bodies kg C m^-2 spatial Density of fungal fruiting bodies growing from the litter and soil float animal animal
decay_of_fungal_fruiting_bodies kg C m^-2 day^-1 spatial Rate of decay of fungal fruiting bodies back into the soil float soil animal animal
production_of_fungal_fruiting_bodies kg C m^-2 day^-1 spatial Rate at which fungal fruiting bodies are produced by soil fungi float soil animal soil
plant_pft_propagules count spatial Per cell counts of propagules for each plant functional type integer plants plants
fallen_non_propagule_c_mass kg C m^-2 spatial Plant reproductive tissue non-propagule turnover since last update float
stem_lignin unitless spatial Proportion of stem carbon that is lignin carbon float litter plants plants
senesced_leaf_lignin unitless spatial Proportion of carbon in leaf turnover that is lignin carbon float litter plants plants
plant_reproductive_tissue_lignin unitless spatial Proportion of carbon in reproductive tissue turnover that is lignin carbon float plants plants
root_lignin unitless spatial Proportion of carbon in root turnover that is lignin carbon float litter plants plants
plant_reproductive_tissue_turnover_c_n_ratio - spatial Carbon:nitrogen ratio of plant reproductive tissue turnover float
plant_reproductive_tissue_turnover_c_p_ratio - spatial Carbon:phosphorus ratio of plant reproductive tissue turnover float
plant_rt_turnover_n_mass kg N spatial Mass of Nitrogen in plant reproductive and tissue turnover float
plant_rt_turnover_p_mass kg P spatial Mass of Phosphorus in plant reproductive and tissue turnover float
plant_reproductive_tissue_turnover kg C spatial Mass of plant reproductive tissue turnover float
plant_reproductive_tissue_turnover_cnp kg C spatial Biomasses of plant reproductive tissue turnover float
fruit_turnover_cnp kg C spatial Biomasses of plant fruit tissue turnover float animal plants plants
seed_turnover_cnp kg C spatial Biomasses of plant seed tissue turnover float animal plants plants
plant_symbiote_carbon_supply kg C m^-2 day^-1 spatial Rate at which plants are supplying carbon to their soil-living symbiotic partners float soil plants plants
root_carbohydrate_exudation kg C m^-2 day^-1 spatial Rate at which plants exude carbohydrates from their roots into the soil float soil plants plants
dissolved_nitrate kg{N} m^-3 spatial Concentration of dissolved nitrate in the topsoil layer float soil plants soil
dissolved_ammonium kg{N} m^-3 spatial Concentration of dissolved ammonium in the topsoil layer float soil plants soil
dissolved_phosphorus kg{P} m^-3 spatial Concentration of dissolved labile inorganic phosphorus in the topsoil layer float soil plants soil
arbuscular_mycorrhizal_n_supply kg{N} spatial Amount of nitrogen provided by arbuscular mycorrhizal fungi to their plant partners float soil plants soil
arbuscular_mycorrhizal_p_supply kg{P} spatial Amount of phosphorous provided by arbuscular mycorrhizal fungi to their plant partners float soil plants soil
ectomycorrhizal_n_supply kg{N} spatial Amount of nitrogen provided by ectomycorrhizal fungi to their plant partners float soil plants soil
ectomycorrhizal_p_supply kg{P} spatial Amount of phosphorous provided by ectomycorrhizal fungi to their plant partners float soil plants soil
plant_ammonium_uptake kg N m^-2 day^-1 spatial Rate at which plants uptake ammonium from the soil float soil plants plants
plant_nitrate_uptake kg N m^-2 day^-1 spatial Rate at which plants uptake nitrate from the soil float soil plants plants
plant_phosphorus_uptake kg P m^-2 day^-1 spatial Rate at which plants uptake labile inorganic phosphorus from the soil float soil plants plants
clay_fraction - spatial The fraction of clay in soil. This is a proportion between 0 and 1. float soil soil
layer_fapar - spatial The fraction of absorbed photosynthetically active radiation (f_APAR) in each model layer. float plants plants
layer_leaf_mass kg spatial The leaf mass within each canopy layer. float plants plants
soil_enzyme_pom_bacteria kg{C} m^-3 spatial Amount of bacterial enzyme class which breaks down particulate organic matter float soil soil soil
soil_enzyme_maom_bacteria kg{C} m^-3 spatial Amount of bacterial enzyme class which breaks down mineral associated organic matter float soil soil soil
soil_enzyme_pom_fungi kg{C} m^-3 spatial Amount of fungal enzyme class which breaks down particulate organic matter float soil soil soil
soil_enzyme_maom_fungi kg{C} m^-3 spatial Amount of fungal enzyme class which breaks down mineral associated organic matter float soil soil soil
subcanopy_vegetation_biomass kg C m^-2 spatial Carbon biomass of vegetation growing underneath the canopy. float plants plants plants
subcanopy_seedbank_biomass kg C m^-2 spatial Carbon biomass of subcanopy seedbank. float plants plants plants
subcanopy_vegetation_litter_lignin unitless spatial Proportion of subcanopy vegetation litter carbon that is lignin carbon. float plants plants
subcanopy_seedbank_litter_lignin unitless spatial Proportion of subcanopy seedbank litter carbon that is lignin carbon float plants plants
subcanopy_ammonium_uptake kg spatial Uptake of ammonium by subcanopy transpiration float soil plants plants
subcanopy_nitrate_uptake kg spatial Uptake of nitrate by subcanopy transpiration float soil plants plants
subcanopy_phosphorus_uptake kg spatial Uptake of phosphorous by subcanopy transpiration float soil plants plants
stem_turnover_cnp kg spatial C, N, and P masses for stem turnover in a given timestep float plants litter plants
foliage_turnover_cnp kg spatial C, N, and P masses for foliage turnover in a given timestep float animal plants litter plants
root_turnover_cnp kg spatial C, N, and P masses for root turnover in a given timestep float plants litter plants
subcanopy_vegetation_litter_cnp kg spatial C, N, and P masses for subcanopy turnover in a given timestep float plants plants
subcanopy_vegetation_cnp kg spatial C, N, and P masses for subcanopy vegetation float animal plants plants
subcanopy_vegetation_cnp_consumed kg C m^-2 spatial C, N, and P masses of subcanopy vegetation consumed by animals. float animal plants animal
subcanopy_seedbank_litter_cnp kg spatial C, N, and P masses for the ground seedbank float plants plants
subcanopy_seedbank_cnp_consumed kg C m^-2 spatial C, N, and P masses of subcanopy seedbank consumed by animals. float animal plants animal
subcanopy_seedbank_cnp kg spatial C, N, and P masses for the subcanopy seedbank CNP float animal plants plants
canopy_fruit_n count spatial Number of fruits of each PFT in the canopy float plants plants
canopy_seeds_per_fruit count spatial Number of seeds per fruit in each PFT float plants plants
canopy_seed_cnp kg spatial C, N, and P of each seed PFT float animal plants plants
fallen_fruit_n count spatial Number of fallen fruits per PFT float plants plants
canopy_fruit_cnp kg spatial Average C, N, and P masses of each fruit per PFT in the canopy float animal plants plants
fallen_fruit_cnp kg spatial Average C, N, and P masses of each fruit per PFT float plants plants
fallen_seeds_per_fruit count spatial Number of seeds per fruit per PFT float plants plants
fallen_seeds_cnp kg spatial Average C, N, and P masses of each seed in a PFT float plants plants
canopy_foliage_cnp kg spatial C, N, and P of canopy foliage float animal plants plants
canopy_foliage_cnp_consumed kg spatial C, N, and P of canopy foliage consumed by animals float animal plants animal
canopy_seed_cnp_consumed kg spatial C, N, and P of canopy seed consumed by animals float animal plants animal
canopy_fruit_cnp_consumed kg spatial C, N, and P of canopy fruit consumed by animals float animal plants animal
foliage_turnover_cnp_consumed kg spatial C, N, and P of foliage turnover consumed by animals float animal plants animal
seed_turnover_cnp_consumed kg spatial C, N, and P of seed turnover consumed by animals float animal plants animal
fruit_turnover_cnp_consumed kg spatial C, N, and P of fruit turnover consumed by animals float animal plants animal
fallen_n_propagules NEEDS UNIT spatial NEEDS DESCRIPTION float
canopy_n_propagules NEEDS UNIT spatial NEEDS DESCRIPTION float
canopy_non_propagule_c_mass NEEDS UNIT spatial NEEDS DESCRIPTION float
sensible_heat_flux_topofcanopy NEEDS UNIT spatial NEEDS DESCRIPTION float
surface_runoff_accumulated NEEDS UNIT spatial NEEDS DESCRIPTION float
molar_density_air NEEDS UNIT spatial NEEDS DESCRIPTION float
subsurface_flow_accumulated NEEDS UNIT spatial NEEDS DESCRIPTION - I THINK THIS MIGHT BE AN OUTDATED INPUT INTO ANIMALS float
zero_displacement_height NEEDS UNIT spatial NEEDS DESCRIPTION - I THINK THIS MIGHT BE AN OUTDATED INPUT INTO ANIMALS float
aerodynamic_resistance_surface NEEDS UNIT spatial NEEDS DESCRIPTION - I THINK THIS MIGHT BE AN OUTDATED INPUT INTO ANIMALS float
absorbed_radiation NEEDS UNIT spatial NEEDS DESCRIPTION - I THINK THIS MIGHT BE AN OUTDATED INPUT INTO ANIMALS float
evapotranspiration NEEDS UNIT spatial NEEDS DESCRIPTION - I THINK THIS MIGHT BE AN OUTDATED INPUT INTO ANIMALS float