Index

_

__contains__() (virtual_ecosystem.core.data.Data method) __getitem__() (virtual_ecosystem.core.data.Data method) __init__() (virtual_ecosystem.core.base_model.BaseDisturbance method) (virtual_ecosystem.core.base_model.BaseModel method) __init_subclass__() (virtual_ecosystem.core.axes.AxisValidator class method) (virtual_ecosystem.core.base_model.BaseDisturbance class method) (virtual_ecosystem.core.base_model.BaseModel class method) __post_init__() (virtual_ecosystem.core.core_components.CoreComponents method) (virtual_ecosystem.core.core_components.LayerStructure method) (virtual_ecosystem.core.core_components.ModelTiming method) __repr__() (docstring_style.MyClass method) (virtual_ecosystem.core.base_model.BaseDisturbance method) (virtual_ecosystem.core.base_model.BaseModel method) (virtual_ecosystem.core.data.Data method) (virtual_ecosystem.core.grid.Grid method) __setitem__() (virtual_ecosystem.core.data.Data method) __str__() (virtual_ecosystem.core.base_model.BaseModel method)

_check_model_name() (virtual_ecosystem.core.base_model.BaseDisturbance class method) (virtual_ecosystem.core.base_model.BaseModel class method) _check_model_update_bounds() (virtual_ecosystem.core.base_model.BaseModel class method) _check_variables_attribute() (virtual_ecosystem.core.base_model.BaseModel class method) _collect_config_paths() (virtual_ecosystem.core.config_builder.ConfigurationLoader method) _compile_data() (virtual_ecosystem.core.config_builder.ConfigurationLoader method) _load_config_toml() (virtual_ecosystem.core.config_builder.ConfigurationLoader method) _load_config_toml_string() (virtual_ecosystem.core.config_builder.ConfigurationLoader method) _load_data() (virtual_ecosystem.core.config_builder.ConfigurationLoader method) _parse_cli_paths() (in module virtual_ecosystem.entry_points) _parse_command_line_config() (in module virtual_ecosystem.entry_points) _parse_config_string() (in module virtual_ecosystem.entry_points) _resolve_config_file_paths() (virtual_ecosystem.core.config_builder.ConfigurationLoader method) _resolve_config_paths() (in module virtual_ecosystem.core.config_builder) _role_indices_bool (virtual_ecosystem.core.core_components.LayerStructure attribute) _role_indices_int (virtual_ecosystem.core.core_components.LayerStructure attribute) _setup() (virtual_ecosystem.core.base_model.BaseModel method)

A

a_class_attribute (docstring_style.MyClass attribute) abandon_communities() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) AbioticConfiguration (class in virtual_ecosystem.models.abiotic.model_config) AbioticConstants (class in virtual_ecosystem.models.abiotic.model_config) AbioticModel (class in virtual_ecosystem.models.abiotic.abiotic_model) AbioticSharedConstants (class in virtual_ecosystem.models.abiotic_simple.model_config) AbioticSimpleBounds (class in virtual_ecosystem.models.abiotic_simple.model_config) AbioticSimpleConfiguration (class in virtual_ecosystem.models.abiotic_simple.model_config) AbioticSimpleConstants (class in virtual_ecosystem.models.abiotic_simple.model_config) AbioticSimpleModel (class in virtual_ecosystem.models.abiotic_simple.abiotic_simple_model) above_canopy_height_offset (virtual_ecosystem.core.core_components.LayerStructure attribute) (virtual_ecosystem.core.model_config.LayersConfiguration attribute) above_metabolic (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) above_metabolic_carbon (virtual_ecosystem.models.litter.losses.LitterLosses attribute) above_metabolic_nitrogen (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) above_metabolic_phosphorus (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) above_structural (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) above_structural_carbon (virtual_ecosystem.models.litter.losses.LitterLosses attribute) above_structural_lignin (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) above_structural_nitrogen (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) above_structural_phosphorus (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) activation_energy_rate (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) activation_energy_saturation (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) activation_energy_turnover (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) activation_energy_uptake_rate (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) activation_energy_uptake_saturation (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) active_cohorts (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) activity_window() (in module virtual_ecosystem.models.animal.scaling_functions) actual_element_mass (virtual_ecosystem.models.plants.biomasses.Element attribute) add_carcass() (virtual_ecosystem.models.animal.decay.CarcassPool method) add_elemental_masses() (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC method) add_excrement() (virtual_ecosystem.models.animal.decay.ExcrementPool method) add_file_logger() (in module virtual_ecosystem.core.logger) add_from_dict() (virtual_ecosystem.core.data.Data method) add_mass() (virtual_ecosystem.models.plants.subcanopy.SubcanopyBiomass method) add_note() (virtual_ecosystem.models.soil.soil_model.IntegrationError method) add_waste() (virtual_ecosystem.models.animal.decay.HerbivoryWaste method) adult_mass (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) advect_water_from_toplayer() (in module virtual_ecosystem.models.abiotic.wind) aerodynamic_resistance_canopy_day (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) aerodynamic_resistance_canopy_night (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) aerodynamic_resistance_soil_night (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) age (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) air_entry_potential_inverse (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) air_temperature (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSimpleBounds attribute) air_volumetric_heat_capacity (virtual_ecosystem.core.model_config.CoreConstants attribute) allocate_gpp() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) allocations (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) alpha_0_herb (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) alpha_0_pred (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) alpha_i_j() (in module virtual_ecosystem.models.animal.scaling_functions)

alpha_i_k() (in module virtual_ecosystem.models.animal.scaling_functions) ammonia_volatilisation_rate_constant (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) ammonium (virtual_ecosystem.models.soil.pools.LitterMineralisationFluxes attribute) (virtual_ecosystem.models.soil.pools.WaterRemovalRates attribute) (virtual_ecosystem.models.soil.uptake.MaxUptakeRates attribute) (virtual_ecosystem.models.soil.uptake.NetNutrientConsumption attribute) ammonium_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) ammonium_deposition_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) ammonium_mineralisation_proportion (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) AN_OBJECT (in module docstring_style) animal_cohort_exporter (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) AnimalCohort (class in virtual_ecosystem.models.animal.animal_cohorts) AnimalCohortDataExporter (class in virtual_ecosystem.models.animal.exporter) AnimalConfiguration (class in virtual_ecosystem.models.animal.model_config) AnimalConstants (class in virtual_ecosystem.models.animal.model_config) AnimalExportConfig (class in virtual_ecosystem.models.animal.model_config) AnimalModel (class in virtual_ecosystem.models.animal.animal_model) append() (virtual_ecosystem.models.plants.biomasses.Biomasses method) (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC method) (virtual_ecosystem.models.plants.biomasses.Element method) apply_decay() (virtual_ecosystem.models.animal.decay.FungalFruitPool method) apply_growth() (virtual_ecosystem.models.plants.biomasses.Biomasses method) (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC method) (virtual_ecosystem.models.plants.biomasses.FoliageBiomass method) (virtual_ecosystem.models.plants.biomasses.FruitBiomass method) (virtual_ecosystem.models.plants.biomasses.ReproductiveBiomass method) (virtual_ecosystem.models.plants.biomasses.RootBiomass method) (virtual_ecosystem.models.plants.biomasses.SeedBiomass method) (virtual_ecosystem.models.plants.biomasses.StemBiomass method) apply_herbivory() (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC method) (virtual_ecosystem.models.plants.plants_model.PlantsModel method) apply_mortality() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) apply_recruitment() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) apply_turnover() (virtual_ecosystem.models.plants.biomasses.Biomasses method) aquatic_cohorts (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) aquatic_mortality (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) aquatic_residence_time (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) arbuscular_mycorrhiza (virtual_ecosystem.models.soil.microbial_groups.CarbonSupply attribute) (virtual_ecosystem.models.soil.pools.BiomassLosses attribute) arbuscular_mycorrhiza_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) arbuscular_mycorrhiza_n_supply (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) arbuscular_mycorrhiza_p_supply (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) array_attrs (virtual_ecosystem.models.plants.biomasses.Biomasses attribute) (virtual_ecosystem.models.plants.functional_types.ExtraTraitsPFT attribute) array_resource_pools (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) ARRAY_RESOURCES (in module virtual_ecosystem.models.animal.array_resources) array_resources (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) ArrayResource (class in virtual_ecosystem.models.animal.array_resources) ArrayResourceDefinition (class in virtual_ecosystem.models.animal.array_resources) as_array() (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC method) assign_prey_groups() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) available water capacity available_attributes (virtual_ecosystem.models.animal.exporter.AnimalCohortDataExporter attribute) (virtual_ecosystem.models.plants.exporter.CommunityDataExporter attribute) average_nutrient_ratios() (in module virtual_ecosystem.models.litter.inputs) average_temperature_over_microbially_active_layers() (in module virtual_ecosystem.models.litter.env_factors) average_water_potential_over_microbially_active_layers() (in module virtual_ecosystem.models.litter.env_factors) axis (virtual_ecosystem.core.variables.VariableMetadata attribute) AXIS_VALIDATORS (in module virtual_ecosystem.core.axes) AxisValidator (class in virtual_ecosystem.core.axes)

B

b_herb (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) b_pred (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) background_mortality() (in module virtual_ecosystem.models.animal.scaling_functions) bacteria (virtual_ecosystem.models.soil.pools.BiomassLosses attribute) bacteria_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) balance_elements() (virtual_ecosystem.models.plants.biomasses.Biomasses method) base_soil_protection (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) BaseDisturbance (class in virtual_ecosystem.core.base_model) BaseModel (class in virtual_ecosystem.core.base_model) below_canopy_light_fraction (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) below_metabolic (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) below_metabolic_carbon (virtual_ecosystem.models.litter.losses.LitterLosses attribute) below_metabolic_nitrogen (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) below_metabolic_phosphorus (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) below_structural (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) below_structural_carbon (virtual_ecosystem.models.litter.losses.LitterLosses attribute) below_structural_lignin (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) below_structural_nitrogen (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) below_structural_phosphorus (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute)

beta_responsive_bodymass (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) bfs_territory() (in module virtual_ecosystem.models.animal.scaling_functions) biomass_density_to_individuals() (in module virtual_ecosystem.models.animal.scaling_functions) biomass_tissues (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) Biomasses (class in virtual_ecosystem.models.plants.biomasses) biomasses (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) BiomassLosses (class in virtual_ecosystem.models.soil.pools) BiomassTissueABC (class in virtual_ecosystem.models.plants.biomasses) birth() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) birth_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) birth_mass (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) birth_mass_threshold (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) boltzmann_constant (virtual_ecosystem.core.model_config.CoreConstants attribute) bounds (virtual_ecosystem.core.grid.Grid attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic.model_config.AbioticConfiguration attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) broad_diet (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) build_configuration_model() (in module virtual_ecosystem.core.config_builder) build_indices() (in module virtual_ecosystem.models.abiotic.abiotic_tools) build_microbial_group() (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants class method) build_output_from_record() (in module virtual_ecosystem.models.abiotic.microclimate) bulk_density_soil (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) bypass_flow_coefficient (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute)

C

c_n_ratio (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) c_p_ratio (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) c_tol (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) c_tsm (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) c_x_ratio() (virtual_ecosystem.models.plants.subcanopy.SubcanopyBiomass method) calculate_absorbed_longwave_radiation() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_actual_carbon_gain() (in module virtual_ecosystem.models.soil.uptake) calculate_actual_vapour_pressure() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_aerodynamic_resistance() (in module virtual_ecosystem.models.abiotic.wind) calculate_aerodynamic_resistance_understorey() (in module virtual_ecosystem.models.abiotic.wind) calculate_air_density() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_all_pool_updates() (virtual_ecosystem.models.soil.pools.SoilPools method) calculate_alpha() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) calculate_atmospheric_layer_geometry() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_biomass_losses() (in module virtual_ecosystem.models.soil.pools) calculate_birth_mass_cnp() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) calculate_bypass_flow() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_canopies() (in module virtual_ecosystem.models.plants.canopy) calculate_canopy_evaporation() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_carbon_mineralised() (in module virtual_ecosystem.models.litter.carbon) calculate_carbon_pool_loss() (in module virtual_ecosystem.models.litter.losses) calculate_carbon_use_efficiency() (in module virtual_ecosystem.models.soil.env_factors) calculate_clay_impact_on_enzyme_saturation() (in module virtual_ecosystem.models.soil.env_factors) calculate_consumed_mass_predation() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) calculate_decay_rates() (in module virtual_ecosystem.models.litter.carbon) calculate_denitrification_temperature_factor() (in module virtual_ecosystem.models.soil.env_factors) calculate_density_for_cohort() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) calculate_dissolved_nutrient_concentrations() (virtual_ecosystem.models.soil.soil_model.SoilModel method) calculate_drainage_map() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_dynamics() (virtual_ecosystem.models.plants.subcanopy.Subcanopy method) calculate_effective_saturation() (in module virtual_ecosystem.models.hydrology.hydrology_tools) calculate_energy_balance_residual() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_environmental_effect_factors() (in module virtual_ecosystem.models.soil.env_factors) calculate_environmental_factors() (in module virtual_ecosystem.models.litter.env_factors) calculate_enzyme_changes() (in module virtual_ecosystem.models.soil.pools) calculate_enzyme_mediated_decomposition() (in module virtual_ecosystem.models.soil.pools) calculate_enzyme_mediated_rates() (in module virtual_ecosystem.models.soil.pools) calculate_enzyme_production() (in module virtual_ecosystem.models.soil.pools) calculate_enzyme_turnover() (in module virtual_ecosystem.models.soil.pools) calculate_final_pool_size() (in module virtual_ecosystem.models.litter.carbon) calculate_free_living_nitrogen_fixation() (in module virtual_ecosystem.models.soil.pools) calculate_friction_velocity() (in module virtual_ecosystem.models.abiotic.wind) calculate_fruiting_body_production() (in module virtual_ecosystem.models.soil.pools) calculate_fungal_fruiting_body_decay() (in module virtual_ecosystem.models.soil.pools) calculate_highest_achievable_nutrient_uptake() (in module virtual_ecosystem.models.soil.uptake) calculate_initial_symbiotic_supply() (virtual_ecosystem.models.soil.soil_model.SoilModel method) calculate_input_chemistries() (in module virtual_ecosystem.models.litter.inputs) calculate_interception() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_latent_heat_flux() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_latent_heat_vapourisation() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_light_use_efficiency() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) calculate_lignin_pool_loss() (in module virtual_ecosystem.models.litter.losses) calculate_litter_additions_from_herbivory() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) calculate_litter_chemistry_factor() (in module virtual_ecosystem.models.litter.chemistry) calculate_litter_decay_metabolic_above() (in module virtual_ecosystem.models.litter.carbon) calculate_litter_decay_metabolic_below() (in module virtual_ecosystem.models.litter.carbon) calculate_litter_decay_structural_above() (in module virtual_ecosystem.models.litter.carbon) calculate_litter_decay_structural_below() (in module virtual_ecosystem.models.litter.carbon) calculate_litter_decay_woody() (in module virtual_ecosystem.models.litter.carbon) calculate_litter_input_lignin_concentrations() (in module virtual_ecosystem.models.litter.inputs) calculate_litter_input_nutrient_masses() (in module virtual_ecosystem.models.litter.inputs) calculate_litter_losses() (in module virtual_ecosystem.models.litter.losses) calculate_litter_mineralisation_fluxes() (in module virtual_ecosystem.models.soil.pools) calculate_litter_mineralisation_split() (in module virtual_ecosystem.models.soil.pools) calculate_longwave_emission() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_maintenance_biomass_synthesis() (in module virtual_ecosystem.models.soil.pools) calculate_maom_desorption() (in module virtual_ecosystem.models.soil.pools) calculate_matric_potential() (in module virtual_ecosystem.models.hydrology.below_ground) calculate_maximum_uptake_rates() (in module virtual_ecosystem.models.soil.uptake) calculate_metabolic_proportions_of_input() (in module virtual_ecosystem.models.litter.inputs) calculate_microbial_changes() (in module virtual_ecosystem.models.soil.pools) calculate_mixing_coefficients_canopy() (in module virtual_ecosystem.models.abiotic.wind) calculate_molar_density_air() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_necromass_breakdown() (in module virtual_ecosystem.models.soil.pools) calculate_net_enzyme_change() (in module virtual_ecosystem.models.soil.pools) calculate_net_formation_of_secondary_P() (in module virtual_ecosystem.models.soil.pools) calculate_net_nutrient_transfers_from_maom_to_lmwc() (in module virtual_ecosystem.models.soil.pools) calculate_new_biomass_average_nutrient_ratios() (in module virtual_ecosystem.models.soil.microbial_groups) calculate_new_lignin_proportions() (virtual_ecosystem.models.litter.chemistry.LitterChemistry method) calculate_new_pool_chemistries() (virtual_ecosystem.models.litter.chemistry.LitterChemistry method) calculate_nitrification_moisture_factor() (in module virtual_ecosystem.models.soil.env_factors) calculate_nitrification_temperature_factor() (in module virtual_ecosystem.models.soil.env_factors) calculate_nutrient_flows_to_necromass() (in module virtual_ecosystem.models.soil.pools) calculate_nutrient_pool_loss() (in module virtual_ecosystem.models.litter.losses) calculate_nutrient_removal_by_water() (in module virtual_ecosystem.models.soil.pools) calculate_nutrient_split() (in module virtual_ecosystem.models.litter.inputs) calculate_nutrient_uptake() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) calculate_nutrient_uptake_rates() (in module virtual_ecosystem.models.soil.uptake) calculate_offspring_count() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) calculate_pH_suitability() (in module virtual_ecosystem.models.soil.env_factors) calculate_post_consumption_pools() (in module virtual_ecosystem.models.litter.carbon) calculate_potential_prey_consumed() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) calculate_predation_search_rate() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) calculate_predation_success_probability() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) calculate_psychrometric_constant() (in module virtual_ecosystem.models.hydrology.hydrology_tools) calculate_rate_of_denitrification() (in module virtual_ecosystem.models.soil.pools) calculate_rate_of_nitrification() (in module virtual_ecosystem.models.soil.pools) calculate_roughness_length_momentum() (in module virtual_ecosystem.models.abiotic.wind) calculate_semelparous_mass_loss() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) calculate_sensible_heat_flux() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_slope_of_saturated_pressure_curve() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_soil_additions() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) calculate_soil_evaporation() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_soil_fluxes() (in module virtual_ecosystem.models.abiotic.microclimate) calculate_soil_nutrient_mineralisation() (in module virtual_ecosystem.models.soil.pools) calculate_soil_water_effect_on_litter_decomp() (in module virtual_ecosystem.models.litter.env_factors) calculate_solute_removal_by_soil_water() (in module virtual_ecosystem.models.soil.env_factors) calculate_sorption_to_maom() (in module virtual_ecosystem.models.soil.pools) calculate_specific_humidity() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_surface_runoff() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_symbiotic_carbon_supply() (in module virtual_ecosystem.models.soil.microbial_groups) calculate_symbiotic_nitrogen_fixation() (in module virtual_ecosystem.models.soil.pools) calculate_symbiotic_nitrogen_fixation_carbon_cost() (in module virtual_ecosystem.models.soil.env_factors) calculate_temperature_effect_on_litter_decomp() (in module virtual_ecosystem.models.litter.env_factors) calculate_temperature_effect_on_microbes() (in module virtual_ecosystem.models.soil.env_factors) calculate_thermodynamics() (in module virtual_ecosystem.models.abiotic.microclimate) calculate_theta_opt_i() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) calculate_total_absorbed_shortwave_radiation() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_total_C_mineralised() (in module virtual_ecosystem.models.litter.carbon) calculate_total_handling_time_for_herbivory() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) calculate_total_handling_time_for_predation() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) calculate_total_litter_consumption() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) calculate_total_reproductive_mass() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) calculate_total_soil_consumption() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) calculate_turnover() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) calculate_updated_nutrient_pools() (in module virtual_ecosystem.models.litter.chemistry) calculate_updated_pool_lignin_proportion() (in module virtual_ecosystem.models.litter.chemistry) calculate_updated_pools() (in module virtual_ecosystem.models.litter.carbon) calculate_vapour_pressure_deficit() (in module virtual_ecosystem.models.abiotic_simple.microclimate_simple) calculate_vegetation_fluxes() (in module virtual_ecosystem.models.abiotic.microclimate) calculate_vegetation_temperature() (in module virtual_ecosystem.models.abiotic.microclimate) calculate_ventilation_rate() (in module virtual_ecosystem.models.abiotic.wind) calculate_vertical_flow() (in module virtual_ecosystem.models.hydrology.below_ground) calculate_water_potential_impact_on_microbes() (in module virtual_ecosystem.models.soil.env_factors) calculate_wind_profile() (in module virtual_ecosystem.models.abiotic.wind) calculate_wind_profiles() (in module virtual_ecosystem.models.abiotic.microclimate) calculate_zero_plane_displacement() (in module virtual_ecosystem.models.abiotic.wind) can_forage_on() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) can_prey_on() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) can_validate() (virtual_ecosystem.core.axes.AxisValidator method) (virtual_ecosystem.core.axes.Spat_CellId_Coord_Any method) (virtual_ecosystem.core.axes.Spat_CellId_Dim_Any method) (virtual_ecosystem.core.axes.Spat_XY_Coord_Square method) (virtual_ecosystem.core.axes.Spat_XY_Dim_Square method) (virtual_ecosystem.core.axes.Time method) canopies (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute)

canopy_layers (virtual_ecosystem.core.model_config.LayersConfiguration attribute) canopy_top_radiation (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) carbon (virtual_ecosystem.models.soil.uptake.MaxUptakeRates attribute) (virtual_ecosystem.models.soil.uptake.NetNutrientConsumption attribute) carbon_excreta_proportion (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) carbon_mass (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC attribute) (virtual_ecosystem.models.plants.biomasses.FoliageBiomass attribute) (virtual_ecosystem.models.plants.biomasses.FruitBiomass attribute) (virtual_ecosystem.models.plants.biomasses.ReproductiveBiomass attribute) (virtual_ecosystem.models.plants.biomasses.RootBiomass attribute) (virtual_ecosystem.models.plants.biomasses.SeedBiomass attribute) (virtual_ecosystem.models.plants.biomasses.StemBiomass attribute) carbon_mass_per_propagule (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) CarbonSupply (class in virtual_ecosystem.models.soil.microbial_groups) carcass_pools (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) CarcassPool (class in virtual_ecosystem.models.animal.decay) cell_area (virtual_ecosystem.core.grid.Grid attribute) (virtual_ecosystem.core.model_config.GridConfiguration attribute) cell_id (virtual_ecosystem.core.grid.Grid attribute) (virtual_ecosystem.models.animal.decay.CarcassPool attribute) (virtual_ecosystem.models.animal.decay.ExcrementPool attribute) cell_nx (virtual_ecosystem.core.grid.Grid attribute) (virtual_ecosystem.core.model_config.GridConfiguration attribute) cell_ny (virtual_ecosystem.core.grid.Grid attribute) (virtual_ecosystem.core.model_config.GridConfiguration attribute) CellResource (class in virtual_ecosystem.models.animal.array_resources) centroid_key (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) centroids (virtual_ecosystem.core.grid.Grid attribute) cfg_paths (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) cfg_strings (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) characteristic_dimension_leaf (virtual_ecosystem.core.model_config.CoreConstants attribute) check_added_variables() (in module virtual_ecosystem.main) check_for_invalid_input_values() (virtual_ecosystem.models.soil.soil_model.SoilModel method) check_init_data() (virtual_ecosystem.core.base_model.BaseModel method) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel method) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel method) (virtual_ecosystem.models.animal.animal_model.AnimalModel method) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel method) (virtual_ecosystem.models.litter.litter_model.LitterModel method) (virtual_ecosystem.models.plants.plants_model.PlantsModel method) (virtual_ecosystem.models.soil.soil_model.SoilModel method) check_monthly_mass_balance() (in module virtual_ecosystem.models.hydrology.hydrology_tools) check_outfile() (in module virtual_ecosystem.core.utils) check_precipitation_surface() (in module virtual_ecosystem.models.hydrology.hydrology_tools) check_run() (virtual_ecosystem.core.core_components.DisturbanceTiming method) clamp_variable_within_limits() (in module virtual_ecosystem.models.abiotic.wind) clay_saturation (virtual_ecosystem.models.soil.env_factors.EnvironmentalEffectFactors attribute) cleanup() (virtual_ecosystem.core.base_model.BaseModel method) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel method) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel method) (virtual_ecosystem.models.animal.animal_model.AnimalModel method) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel method) (virtual_ecosystem.models.litter.litter_model.LitterModel method) (virtual_ecosystem.models.plants.plants_model.PlantsModel method) (virtual_ecosystem.models.soil.soil_model.SoilModel method) cli_config (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) CNP (class in virtual_ecosystem.models.animal.cnp) cnp_proportion_terms (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) cnp_proportions (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) coarse_category() (virtual_ecosystem.models.animal.animal_traits.DietType method) cohort_attributes (virtual_ecosystem.models.animal.exporter.AnimalCohortDataExporter attribute) (virtual_ecosystem.models.plants.exporter.CommunityDataExporter attribute) (virtual_ecosystem.models.plants.model_config.PlantsExportConfig attribute) cohort_data_path (virtual_ecosystem.models.plants.model_config.PlantsConfiguration attribute) combine_input_sources() (in module virtual_ecosystem.models.litter.inputs) communities (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) community (virtual_ecosystem.models.plants.biomasses.Biomasses attribute) (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC attribute) (virtual_ecosystem.models.plants.biomasses.FoliageBiomass attribute) (virtual_ecosystem.models.plants.biomasses.FruitBiomass attribute) (virtual_ecosystem.models.plants.biomasses.ReproductiveBiomass attribute) (virtual_ecosystem.models.plants.biomasses.RootBiomass attribute) (virtual_ecosystem.models.plants.biomasses.SeedBiomass attribute) (virtual_ecosystem.models.plants.biomasses.StemBiomass attribute) community_canopy_attributes (virtual_ecosystem.models.plants.exporter.CommunityDataExporter attribute) (virtual_ecosystem.models.plants.model_config.PlantsExportConfig attribute) community_data_export (virtual_ecosystem.models.plants.model_config.PlantsConfiguration attribute) CommunityDataExporter (class in virtual_ecosystem.models.plants.exporter) compile_configuration_data() (in module virtual_ecosystem.core.config_builder) CompiledConfiguration (class in virtual_ecosystem.core.configuration) compute_aboveground_layer_thickness() (in module virtual_ecosystem.models.abiotic.abiotic_tools) compute_layer_thickness_for_varying_canopy() (in module virtual_ecosystem.models.abiotic.abiotic_tools) compute_weights_from_absorbed_radiation() (in module virtual_ecosystem.models.abiotic.abiotic_tools) conductance_to_resistance_conversion_factor (virtual_ecosystem.core.model_config.CoreConstants attribute) config (virtual_ecosystem.core.core_components.CoreComponents attribute) (virtual_ecosystem.core.core_components.LayerStructure attribute) (virtual_ecosystem.core.core_components.ModelTiming attribute) (virtual_ecosystem.core.registry.ModuleInfo attribute) config_errors (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) Configuration (class in virtual_ecosystem.core.configuration) ConfigurationError ConfigurationLoader (class in virtual_ecosystem.core.config_builder) confirm_variables_form_data_frame() (in module virtual_ecosystem.core.utils) constants (virtual_ecosystem.core.model_config.CoreConfiguration attribute) (virtual_ecosystem.models.abiotic.model_config.AbioticConfiguration attribute) (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) (virtual_ecosystem.models.animal.model_config.AnimalConfiguration attribute) (virtual_ecosystem.models.hydrology.model_config.HydrologyConfiguration attribute) (virtual_ecosystem.models.litter.model_config.LitterConfiguration attribute) (virtual_ecosystem.models.plants.model_config.PlantsConfiguration attribute) (virtual_ecosystem.models.soil.model_config.SoilConfiguration attribute) construct_full_soil_model() (in module virtual_ecosystem.models.soil.soil_model) consumed_array (virtual_ecosystem.models.animal.array_resources.ArrayResource attribute) (virtual_ecosystem.models.animal.array_resources.ArrayResourceDefinition attribute) consumed_mass (virtual_ecosystem.models.animal.array_resources.ResourcePool attribute) Consumer (class in virtual_ecosystem.models.animal.protocols) convergence_tolerance_secant_solver (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) conversion_efficiency (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) convert_fruiting_body_production_to_rate() (virtual_ecosystem.models.soil.soil_model.SoilModel method) convert_mm_flow_to_m3_per_second() (in module virtual_ecosystem.models.hydrology.above_ground) convert_mycorrhizal_supplies_to_mass() (virtual_ecosystem.models.soil.soil_model.SoilModel method) convert_to_input_masses_to_rates_per_area() (in module virtual_ecosystem.models.litter.inputs) convert_to_litter_units() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) convert_to_soil_units() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) core (virtual_ecosystem.core.model_config.PyrealmConfig attribute) core_axis (virtual_ecosystem.core.axes.AxisValidator attribute) (virtual_ecosystem.core.axes.Spat_CellId_Coord_Any attribute) (virtual_ecosystem.core.axes.Spat_CellId_Dim_Any attribute) (virtual_ecosystem.core.axes.Spat_XY_Coord_Square attribute) (virtual_ecosystem.core.axes.Spat_XY_Dim_Square attribute) (virtual_ecosystem.core.axes.Time attribute) core_constants (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.core.core_components.CoreComponents attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.pools.SoilPools attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) CoreComponents (class in virtual_ecosystem.core.core_components) CoreConfiguration (class in virtual_ecosystem.core.model_config) CoreConstants (class in virtual_ecosystem.core.model_config) count_dietary_categories() (virtual_ecosystem.models.animal.animal_traits.DietType method) create_from_data() (virtual_ecosystem.models.litter.inputs.LitterInputs class method) create_new_cohort() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) create_offspring() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) cue_metabolic (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) cue_reference_temp (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) cue_structural_above_ground (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) cue_structural_below_ground (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) cue_woody (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) current_temperature (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) Cx_ratio (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC property)

D

damuths_law() (in module virtual_ecosystem.models.animal.scaling_functions) damuths_law_terms (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) Data (class in virtual_ecosystem.core.data) data (virtual_ecosystem.core.base_model.BaseDisturbance attribute) (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) (virtual_ecosystem.core.data.Data attribute) (virtual_ecosystem.core.model_config.CoreConfiguration attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.animal.array_resources.ArrayResource attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.pools.SoilPools attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) data_object_templates (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) data_output_options (virtual_ecosystem.core.model_config.CoreConfiguration attribute) data_variables_disturbed (virtual_ecosystem.core.base_model.BaseDisturbance attribute) DataConfiguration (class in virtual_ecosystem.core.model_config) DataGenerator (class in virtual_ecosystem.core.data) DataOutputConfiguration (class in virtual_ecosystem.core.model_config) DataSource (class in virtual_ecosystem.core.model_config) deadwood_mass (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) debug (virtual_ecosystem.core.model_config.CoreConfiguration attribute) DebugConfiguration (class in virtual_ecosystem.core.model_config) decay_fraction_carcasses (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) decay_fraction_excrement (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) decay_rate_carcasses (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) decay_rate_excrement (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) DecayPool (class in virtual_ecosystem.models.animal.protocols) decomposed_cnp (virtual_ecosystem.models.animal.decay.CarcassPool attribute) (virtual_ecosystem.models.animal.decay.ExcrementPool attribute) decomposed_nutrient_per_area() (virtual_ecosystem.models.animal.decay.CarcassPool method) (virtual_ecosystem.models.animal.decay.ExcrementPool method) default_init() (virtual_ecosystem.models.plants.biomasses.Biomasses class method) defecate() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) deficit (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC property) delta_mass_bacteriophagy() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) delta_mass_carcass_scavenging() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) delta_mass_detritivory() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) delta_mass_excrement_scavenging() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) delta_mass_fruiting_fungivory() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) delta_mass_herbivory() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) delta_mass_pomivory() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) delta_mass_predation() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) delta_mass_soil_fungivory() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) denaturation_maom_bacteria (virtual_ecosystem.models.soil.pools.EnzymePoolChanges attribute) denaturation_maom_fungi (virtual_ecosystem.models.soil.pools.EnzymePoolChanges attribute) denaturation_pom_bacteria (virtual_ecosystem.models.soil.pools.EnzymePoolChanges attribute) denaturation_pom_fungi (virtual_ecosystem.models.soil.pools.EnzymePoolChanges attribute) denitrification_infinite_temperature_factor (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) denitrification_minimum_temperature (virtual_ecosystem.models.soil.model_config.SoilConstants attribute)

denitrification_rate_constant (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) denitrification_thermal_sensitivity (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) denominator_tolerance (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) density (virtual_ecosystem.models.animal.array_resources.ArrayResource attribute) (virtual_ecosystem.models.animal.array_resources.ArrayResourceDefinition attribute) density_individuals_m2 (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) density_scaling_method (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) density_water (virtual_ecosystem.core.model_config.CoreConstants attribute) description (virtual_ecosystem.core.variables.VariableMetadata attribute) deserialise_diet_type() (in module virtual_ecosystem.models.animal.model_config) development_status (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) development_type (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) DevelopmentStatus (class in virtual_ecosystem.models.animal.animal_traits) DevelopmentType (class in virtual_ecosystem.models.animal.animal_traits) die_individual() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) diet (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) diet_category_count (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) diet_type (virtual_ecosystem.models.animal.array_resources.ArrayResource attribute) (virtual_ecosystem.models.animal.array_resources.ArrayResourceDefinition attribute) DietType (class in virtual_ecosystem.models.animal.animal_traits) DietTypeSer (in module virtual_ecosystem.models.animal.model_config) dim_names (virtual_ecosystem.core.axes.AxisValidator attribute) (virtual_ecosystem.core.axes.Spat_CellId_Coord_Any attribute) (virtual_ecosystem.core.axes.Spat_CellId_Dim_Any attribute) (virtual_ecosystem.core.axes.Spat_XY_Coord_Square attribute) (virtual_ecosystem.core.axes.Spat_XY_Dim_Square attribute) (virtual_ecosystem.core.axes.Time attribute) DIRPATH_PLACEHOLDER (in module virtual_ecosystem.core.configuration) discover_disturbances() (in module virtual_ecosystem.core.base_model) discover_models() (in module virtual_ecosystem.core.base_model) dispersal_mass_threshold (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) distribute_monthly_rainfall() (in module virtual_ecosystem.models.hydrology.above_ground) disturb() (virtual_ecosystem.core.base_model.BaseDisturbance method) DISTURBANCE_REGISTRY (in module virtual_ecosystem.core.registry) DisturbanceConfigurationRoot (class in virtual_ecosystem.core.configuration) DisturbanceTiming (class in virtual_ecosystem.core.core_components) disturbed_models (virtual_ecosystem.core.base_model.BaseDisturbance attribute) docstring_style module don (virtual_ecosystem.models.soil.pools.LitterMineralisationFluxes attribute) (virtual_ecosystem.models.soil.pools.WaterRemovalRates attribute) don_uptake (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) dop (virtual_ecosystem.models.soil.pools.LitterMineralisationFluxes attribute) (virtual_ecosystem.models.soil.pools.WaterRemovalRates attribute) dop_uptake (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) drag_coefficient_evaporation (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) drainage_map (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) dry_air_factor (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) dsr_to_ppfd (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) dump() (virtual_ecosystem.core.grid.Grid method) (virtual_ecosystem.models.animal.exporter.AnimalCohortDataExporter method) (virtual_ecosystem.models.animal.exporter.ResourcePoolDataExporter method) (virtual_ecosystem.models.plants.exporter.CommunityDataExporter method) dump_config_toml() (in module virtual_ecosystem.core.docutils) dumps() (virtual_ecosystem.core.grid.Grid method)

E

eat() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) ectomycorrhiza (virtual_ecosystem.models.soil.microbial_groups.CarbonSupply attribute) (virtual_ecosystem.models.soil.pools.BiomassLosses attribute) ectomycorrhiza_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) ectomycorrhiza_n_supply (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) ectomycorrhiza_p_supply (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) ectomycorrhiza_supply_fraction (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) effective saturation effective soil moisture Element (class in virtual_ecosystem.models.plants.biomasses) element_masses (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC attribute) (virtual_ecosystem.models.plants.biomasses.FoliageBiomass attribute) (virtual_ecosystem.models.plants.biomasses.FruitBiomass attribute) (virtual_ecosystem.models.plants.biomasses.ReproductiveBiomass attribute) (virtual_ecosystem.models.plants.biomasses.RootBiomass attribute) (virtual_ecosystem.models.plants.biomasses.SeedBiomass attribute) (virtual_ecosystem.models.plants.biomasses.StemBiomass attribute) element_surpluses (virtual_ecosystem.models.plants.biomasses.Biomasses attribute) elemental_masses (virtual_ecosystem.models.animal.array_resources.ResourcePool attribute) elements (virtual_ecosystem.models.plants.biomasses.Biomasses attribute) (virtual_ecosystem.models.plants.subcanopy.Subcanopy attribute) end_time (virtual_ecosystem.core.core_components.ModelTiming attribute) energy_density (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) energy_percentile_threshold (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute)

EnvironmentalEffectFactors (class in virtual_ecosystem.models.soil.env_factors) enzyme_class_definition (virtual_ecosystem.models.soil.model_config.SoilConfiguration attribute) enzyme_class_definition_path (virtual_ecosystem.models.soil.model_config.SoilConfiguration attribute) enzyme_classes (virtual_ecosystem.models.soil.pools.SoilPools attribute) enzyme_production (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) EnzymeMediatedRates (class in virtual_ecosystem.models.soil.pools) EnzymePoolChanges (class in virtual_ecosystem.models.soil.pools) estimate_gpp() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) estimate_past_mycorrhizal_supply() (in module virtual_ecosystem.models.soil.soil_model) example_data_path (in module virtual_ecosystem) excrement_pools (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) ExcrementPool (class in virtual_ecosystem.models.animal.decay) excrete() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) excretion_type (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) ExcretionType (class in virtual_ecosystem.models.animal.animal_traits) exp_interpolation() (in module virtual_ecosystem.models.abiotic_simple.microclimate_simple) export_toml() (virtual_ecosystem.core.configuration.CompiledConfiguration method) exporter (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) extinction_coefficient_global_radiation (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) extinction_coefficient_longwave (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) extra_pft_traits (virtual_ecosystem.models.plants.biomasses.Biomasses attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) ExtraTraitsPFT (class in virtual_ecosystem.models.plants.functional_types)

F

F_i_j_individual() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) F_i_k() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) FILE_FORMAT_REGISTRY (in module virtual_ecosystem.core.readers) FILEPATH_PLACEHOLDER (in module virtual_ecosystem.core.configuration) fill_layer_template() (in module virtual_ecosystem.models.abiotic.abiotic_tools) filled_canopy_mask (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) find_decay_consumed_split() (in module virtual_ecosystem.models.animal.decay) find_enzyme_substrates() (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants method) find_intersecting_carcass_pools() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) find_last_valid_row() (in module virtual_ecosystem.models.abiotic.abiotic_tools) find_lowest_neighbour() (in module virtual_ecosystem.models.hydrology.above_ground) find_microbial_stoichiometries() (in module virtual_ecosystem.models.animal.cnp) find_necromass_nutrient_outflows() (in module virtual_ecosystem.models.soil.pools) find_net_nutrient_consumptions_free_living() (in module virtual_ecosystem.models.soil.uptake) find_net_nutrient_consumptions_symbiotic() (in module virtual_ecosystem.models.soil.uptake) find_nutrient_split_between_litter_pools() (in module virtual_ecosystem.models.litter.inputs) find_total_soil_moisture_for_microbially_active_depth() (in module virtual_ecosystem.models.soil.env_factors) find_upstream_cells() (in module virtual_ecosystem.models.hydrology.above_ground) find_water_outflow_rates() (in module virtual_ecosystem.models.soil.env_factors) finite_and_within() (in module virtual_ecosystem.models.abiotic.abiotic_tools) float_format (virtual_ecosystem.models.animal.exporter.AnimalCohortDataExporter attribute) (virtual_ecosystem.models.animal.exporter.ResourcePoolDataExporter attribute) (virtual_ecosystem.models.plants.exporter.CommunityDataExporter attribute) (virtual_ecosystem.models.plants.model_config.PlantsExportConfig attribute) flora (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) flow_to_reproductive_mass_threshold (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) FoliageBiomass (class in virtual_ecosystem.models.plants.biomasses) forage_cohort() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) forage_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) forage_resource_list() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) fraction_par_used_for_photosynthesis (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) free_living_N_fixation_q10_coefficent (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) free_living_N_fixation_reference_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) free_living_N_fixation_reference_temp (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) from_cfg_strings (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) from_config() (virtual_ecosystem.core.base_model.BaseDisturbance class method) (virtual_ecosystem.core.base_model.BaseModel class method) (virtual_ecosystem.core.grid.Grid class method) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel class method) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel class method) (virtual_ecosystem.models.animal.animal_model.AnimalModel class method) (virtual_ecosystem.models.animal.exporter.AnimalCohortDataExporter class method) (virtual_ecosystem.models.animal.exporter.ResourcePoolDataExporter class method) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel class method) (virtual_ecosystem.models.litter.litter_model.LitterModel class method) (virtual_ecosystem.models.plants.exporter.CommunityDataExporter class method) (virtual_ecosystem.models.plants.plants_model.PlantsModel class method) (virtual_ecosystem.models.soil.soil_model.SoilModel class method)

from_constants() (virtual_ecosystem.models.plants.subcanopy.Nutrient class method) (virtual_ecosystem.models.plants.subcanopy.SubcanopyBiomass class method) from_df() (virtual_ecosystem.models.plants.functional_types.ExtraTraitsPFT class method) from_dict() (virtual_ecosystem.models.animal.cnp.CNP class method) from_pft_default_ratios() (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC class method) (virtual_ecosystem.models.plants.biomasses.FoliageBiomass class method) (virtual_ecosystem.models.plants.biomasses.FruitBiomass class method) (virtual_ecosystem.models.plants.biomasses.ReproductiveBiomass class method) (virtual_ecosystem.models.plants.biomasses.RootBiomass class method) (virtual_ecosystem.models.plants.biomasses.SeedBiomass class method) (virtual_ecosystem.models.plants.biomasses.StemBiomass class method) from_template() (virtual_ecosystem.core.core_components.LayerStructure method) FruitBiomass (class in virtual_ecosystem.models.plants.biomasses) fruiting_body_production (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) functional_group (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) functional_group_definitions_path (virtual_ecosystem.models.animal.model_config.AnimalConfiguration attribute) functional_groups (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.soil.pools.SoilPools attribute) FunctionalGroup (class in virtual_ecosystem.models.animal.functional_group) fungal_fruiting_bodies (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) fungal_fruiting_bodies_c_n_ratio (virtual_ecosystem.core.model_config.CoreConstants attribute) fungal_fruiting_bodies_c_p_ratio (virtual_ecosystem.core.model_config.CoreConstants attribute) fungal_fruiting_bodies_decay_rate (virtual_ecosystem.core.model_config.CoreConstants attribute) FungalFruitPool (class in virtual_ecosystem.models.animal.decay)

G

gas_constant_water_vapour (virtual_ecosystem.core.model_config.CoreConstants attribute) generate_configuration() (in module virtual_ecosystem.core.config_builder) generate_diurnal_cycle_from_monthly_data() (in module virtual_ecosystem.models.abiotic.abiotic_tools) generate_hourly_forcing() (in module virtual_ecosystem.models.abiotic.microclimate) get_array_resources() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_bacteria_pools() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_carcass_pools() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_distances() (virtual_ecosystem.core.grid.Grid method) get_disturbance_config() (virtual_ecosystem.core.configuration.CompiledConfiguration method) get_eaten() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) (virtual_ecosystem.models.animal.array_resources.CellResource method) (virtual_ecosystem.models.animal.decay.FungalFruitPool method) (virtual_ecosystem.models.animal.decay.ScavengeableMixin method) (virtual_ecosystem.models.animal.decay.SoilPool method) (virtual_ecosystem.models.animal.protocols.Resource method) get_elemental_masses (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC property) get_excess_nutrients() (virtual_ecosystem.models.plants.subcanopy.SubcanopyBiomass method) get_excrement_pools() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_flora_from_config() (in module virtual_ecosystem.models.plants.functional_types) get_functional_group_by_name() (in module virtual_ecosystem.models.animal.functional_group) get_fungal_fruit_pools() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_herbivory_waste_pools() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_mean_territory_climate() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_model_configuration_class() (in module virtual_ecosystem.core.registry) get_model_order() (in module virtual_ecosystem.core.variables) get_plant_resources() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_pom_pools() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_pools() (virtual_ecosystem.models.animal.array_resources.ArrayResource method) get_population_density_terms() (virtual_ecosystem.models.animal.model_config.AnimalConstants method) get_prey() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_proportions() (virtual_ecosystem.models.animal.cnp.CNP method) get_ratios() (virtual_ecosystem.models.animal.cnp.CNP method) get_relative_carbon_biomass_by_pft() (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC method) get_soil_fungi_pools() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method)

get_stratum_climate() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_subconfiguration() (virtual_ecosystem.core.configuration.CompiledConfiguration method) get_territory_cells() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_territory_intersection() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) get_tissue() (virtual_ecosystem.models.plants.biomasses.Biomasses method) get_turnover() (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC method) (virtual_ecosystem.models.plants.biomasses.FoliageBiomass method) (virtual_ecosystem.models.plants.biomasses.FruitBiomass method) (virtual_ecosystem.models.plants.biomasses.ReproductiveBiomass method) (virtual_ecosystem.models.plants.biomasses.RootBiomass method) (virtual_ecosystem.models.plants.biomasses.SeedBiomass method) (virtual_ecosystem.models.plants.biomasses.StemBiomass method) gravitational head gravity (virtual_ecosystem.core.model_config.CoreConstants attribute) Grid (class in virtual_ecosystem.core.grid) grid (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.core.core_components.CoreComponents attribute) (virtual_ecosystem.core.data.Data attribute) (virtual_ecosystem.core.model_config.CoreConfiguration attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) GRID_REGISTRY (in module virtual_ecosystem.core.grid) grid_type (virtual_ecosystem.core.grid.Grid attribute) (virtual_ecosystem.core.model_config.GridConfiguration attribute) GridConfiguration (class in virtual_ecosystem.core.model_config) ground_incident_light_fraction (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) groundwater_capacity (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) groundwater_loss (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) grow() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method)

H

h_herb_0 (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) H_i_j() (in module virtual_ecosystem.models.animal.scaling_functions) H_i_k() (in module virtual_ecosystem.models.animal.scaling_functions) h_pred_0 (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) half_sat_ammonium_uptake (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) half_sat_labile_C_uptake (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) half_sat_labile_p_uptake (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) half_sat_nitrate_uptake (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute)

half_saturation_constant (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) handle_ontogeny() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) handle_post_birth_parent_updates() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) handle_semelparous_parent_death() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) HerbivoryWaste (class in virtual_ecosystem.models.animal.decay) heterotroph_normalization_factor() (in module virtual_ecosystem.models.animal.scaling_functions) HIGHER_TAXONOMIC_GROUPS (in module virtual_ecosystem.models.soil.model_config) highest_optimal_pH_microbes (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) hours_per_day (virtual_ecosystem.core.model_config.CoreConstants attribute) HydrologyConfiguration (class in virtual_ecosystem.models.hydrology.model_config) HydrologyConstants (class in virtual_ecosystem.models.hydrology.model_config) HydrologyModel (class in virtual_ecosystem.models.hydrology.hydrology_model)

I

id (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) ideal_ratio (virtual_ecosystem.models.plants.biomasses.Element attribute) import_functional_groups() (in module virtual_ecosystem.models.animal.functional_group) increase_age() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) increase_age_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) index_above (virtual_ecosystem.core.core_components.LayerStructure property) index_above_scalar (virtual_ecosystem.core.core_components.LayerStructure property) index_active_soil (virtual_ecosystem.core.core_components.LayerStructure property) index_all_soil (virtual_ecosystem.core.core_components.LayerStructure property) index_atmosphere (virtual_ecosystem.core.core_components.LayerStructure property) index_canopy (virtual_ecosystem.core.core_components.LayerStructure property) index_filled_atmosphere (virtual_ecosystem.core.core_components.LayerStructure property) index_filled_canopy (virtual_ecosystem.core.core_components.LayerStructure property) index_flux_layers (virtual_ecosystem.core.core_components.LayerStructure property) index_subsoil (virtual_ecosystem.core.core_components.LayerStructure property) index_surface (virtual_ecosystem.core.core_components.LayerStructure property) index_surface_scalar (virtual_ecosystem.core.core_components.LayerStructure property) index_topsoil (virtual_ecosystem.core.core_components.LayerStructure property) index_topsoil_scalar (virtual_ecosystem.core.core_components.LayerStructure property) individuals (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) inflict_non_predation_mortality() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) inflict_non_predation_mortality_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) inflow initial_aerodynamic_resistance_canopy (virtual_ecosystem.core.model_config.CoreConstants attribute) initial_aerodynamic_resistance_soil (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) initial_cohort_data (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) initial_flux_value (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) initial_groundwater_saturation (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.hydrology.model_config.HydrologyConfiguration attribute)

initial_soil_moisture (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.hydrology.model_config.HydrologyConfiguration attribute) initial_stomatal_conductance (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) InitialisationError initialise_atmosphere_for_hydrology() (in module virtual_ecosystem.models.hydrology.hydrology_tools) initialise_canopy_and_soil_fluxes() (in module virtual_ecosystem.models.abiotic.energy_balance) initialise_canopy_layers() (in module virtual_ecosystem.models.plants.canopy) initialise_disturbances() (in module virtual_ecosystem.main) initialise_models() (in module virtual_ecosystem.main) initialise_soil_moisture_mm() (in module virtual_ecosystem.models.hydrology.hydrology_tools) initialize_data_record() (in module virtual_ecosystem.models.abiotic.abiotic_tools) initialize_hourly_record() (in module virtual_ecosystem.models.abiotic.microclimate) initialize_state() (in module virtual_ecosystem.models.abiotic.microclimate) inorganic_phosphorus (virtual_ecosystem.models.soil.uptake.MaxUptakeRates attribute) (virtual_ecosystem.models.soil.uptake.NetNutrientConsumption attribute) InputChemistries (class in virtual_ecosystem.models.litter.inputs) install_example_directory() (in module virtual_ecosystem.entry_points) integrate() (virtual_ecosystem.models.soil.soil_model.SoilModel method) IntegrationError intercept_parameters (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) interpolate_soil_temperature() (in module virtual_ecosystem.models.abiotic_simple.microclimate_simple) is_alive (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) is_below_mass_threshold() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) is_core (virtual_ecosystem.core.registry.ModuleInfo attribute) is_forageable() (virtual_ecosystem.models.animal.array_resources.ResourcePool method) is_invertebrate (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) is_mature (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) is_migration_season() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) is_vertebrate (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute)

J

J_st (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute)

juvenile_dispersal_speed() (in module virtual_ecosystem.models.animal.scaling_functions)

K

k_i_j() (in module virtual_ecosystem.models.animal.scaling_functions)

k_i_k() (in module virtual_ecosystem.models.animal.scaling_functions) known_variables (virtual_ecosystem.core.data.Data attribute)

L

labile_p (virtual_ecosystem.models.soil.pools.LitterMineralisationFluxes attribute) labile_P (virtual_ecosystem.models.soil.pools.WaterRemovalRates attribute) labile_p_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) labile_phosphorus_sorption_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) lambda_max (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) lambda_se (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) largest_mass_achieved (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) latent_heat_vap_equ_factors (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) latitude (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic.model_config.AbioticConfiguration attribute) layer_indices (virtual_ecosystem.core.core_components.LayerStructure attribute) layer_roles (virtual_ecosystem.core.core_components.LayerStructure attribute) layer_structure (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.core.core_components.CoreComponents attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) layers (virtual_ecosystem.core.model_config.CoreConfiguration attribute) LayersConfiguration (class in virtual_ecosystem.core.model_config) LayerStructure (class in virtual_ecosystem.core.core_components) leaf_absorptance_non_par (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) leaf_albedo (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) leaf_emissivity (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSharedConstants attribute) (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSimpleConstants attribute) leaf_lignin (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) leaf_mass (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) leaf_waste_pools (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) leaves_meta_split (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) lignin_inhibition_factor (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) lignin_proportion (virtual_ecosystem.models.animal.decay.HerbivoryWaste attribute) litter_chemistry (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) litter_decay_constant_metabolic_above (virtual_ecosystem.models.litter.model_config.LitterConstants attribute)

litter_decay_constant_metabolic_below (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) litter_decay_constant_structural_above (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) litter_decay_constant_structural_below (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) litter_decay_constant_woody (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) litter_decay_water_potential_halt (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) litter_decay_water_potential_optimum (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) litter_decomp_offset_temp (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) litter_decomp_reference_temp (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) litter_decomp_temp_response (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) litter_leaching_fraction_carbon (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) litter_leaching_fraction_nitrogen (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) litter_leaching_fraction_phosphorus (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) LitterChemistry (class in virtual_ecosystem.models.litter.chemistry) LitterConfiguration (class in virtual_ecosystem.models.litter.model_config) LitterConstants (class in virtual_ecosystem.models.litter.model_config) LitterInputs (class in virtual_ecosystem.models.litter.inputs) LitterLosses (class in virtual_ecosystem.models.litter.losses) LitterMineralisationFluxes (class in virtual_ecosystem.models.soil.pools) LitterModel (class in virtual_ecosystem.models.litter.litter_model) LMWC lmwc (virtual_ecosystem.models.soil.pools.LitterMineralisationFluxes attribute) (virtual_ecosystem.models.soil.pools.WaterRemovalRates attribute) lmwc_sorption_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) lmwc_uptake (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) load_csv() (in module virtual_ecosystem.core.readers) load_data_config() (virtual_ecosystem.core.data.Data method) load_excel() (in module virtual_ecosystem.core.readers) load_known_variables() (in module virtual_ecosystem.core.variables) load_netcdf() (in module virtual_ecosystem.core.readers) load_to_dataarray() (in module virtual_ecosystem.core.readers) local runoff generation location_status (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) log_interpolation() (in module virtual_ecosystem.models.abiotic_simple.microclimate_simple) LOGGER (in module virtual_ecosystem.core.logger) logit_cue_with_temperature (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) lowest_canopy_filled (virtual_ecosystem.core.core_components.LayerStructure attribute) lowest_optimal_pH_microbes (virtual_ecosystem.models.soil.model_config.SoilConstants attribute)

M

M_disp_ref (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) M_herb_ref (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) M_pred_ref (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) m_to_kpa (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) m_tol (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) m_tsm (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) madingley_biomass_scaling_terms (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) make_canopy_residual() (in module virtual_ecosystem.models.abiotic.energy_balance) make_full_set_of_microbial_groups() (in module virtual_ecosystem.models.soil.microbial_groups) make_hex_grid() (in module virtual_ecosystem.core.grid) make_slices() (in module virtual_ecosystem.models.soil.soil_model) make_square_grid() (in module virtual_ecosystem.core.grid) MAOM maom_desorption_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) maom_enzyme_bacteria_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) maom_enzyme_fungi_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) maom_to_lmwc (virtual_ecosystem.models.soil.pools.EnzymeMediatedRates attribute) map_xy_to_cell_id() (virtual_ecosystem.core.grid.Grid method) map_xy_to_cell_indexing() (virtual_ecosystem.core.grid.Grid method) mass_cnp (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animal.decay.HerbivoryWaste attribute) mass_current (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort property) (virtual_ecosystem.models.animal.array_resources.CellResource property) (virtual_ecosystem.models.animal.decay.CarcassPool property) (virtual_ecosystem.models.animal.decay.ExcrementPool property) (virtual_ecosystem.models.animal.decay.FungalFruitPool property) (virtual_ecosystem.models.animal.decay.SoilPool property) (virtual_ecosystem.models.animal.protocols.Resource property) match_vertical() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) max_depth_of_microbial_activity (virtual_ecosystem.core.core_components.LayerStructure attribute) (virtual_ecosystem.core.model_config.CoreConstants attribute) max_metabolic_fraction_of_input (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) max_mixing_coefficient (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) max_percolation_rate_uzlz (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) max_pH_microbes (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) max_ratio_wind_to_friction_velocity (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) max_uptake_rate_ammonium (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) max_uptake_rate_labile_C (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) max_uptake_rate_labile_p (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) max_uptake_rate_nitrate (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) maximum_rate (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) maxiter_secant_solver (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) MaxUptakeRates (class in virtual_ecosystem.models.soil.uptake) mean_to_layers() (in module virtual_ecosystem.models.abiotic.abiotic_tools) mechanical_efficiency (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) merge_configuration_dicts() (in module virtual_ecosystem.core.config_builder) merge_conflicts (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) merge_continuous_data_files() (in module virtual_ecosystem.core.data) merge_input_lignin_proportions() (in module virtual_ecosystem.models.litter.inputs) metabolic_rate() (in module virtual_ecosystem.models.animal.scaling_functions) metabolic_rate_terms (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) metabolic_scaling_coefficients (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) metabolic_split_nitrogen_sensitivity (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) metabolic_split_phosphorus_sensitivity (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) metabolic_to_structural_n_ratio (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) metabolic_to_structural_p_ratio (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) metabolic_type (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) MetabolicType (class in virtual_ecosystem.models.animal.animal_traits) metabolize() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) metabolize_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) metamorph_mortality (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) metamorphose() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) metamorphose_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) meters_to_mm (virtual_ecosystem.core.model_config.CoreConstants attribute) microbial_c_n_p_ratios (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) microbial_group_definition (virtual_ecosystem.models.soil.model_config.SoilConfiguration attribute) microbial_group_definition_path (virtual_ecosystem.models.soil.model_config.SoilConfiguration attribute) microbial_water_response_curvature (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) MicrobialChanges (class in virtual_ecosystem.models.soil.pools) MicrobialGroupConstants (class in virtual_ecosystem.models.soil.microbial_groups) migrate() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) migrate_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) migrate_external() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) migrate_external_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) migrate_juvenile_probability() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) migrated_cohorts (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) migration_mortality (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) migration_residence_time (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) migration_type (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) MigrationType (class in virtual_ecosystem.models.animal.animal_traits) min_leaf_area_index_for_mixing (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) min_pH_microbes (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) min_roughness_length (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) min_specific_humidity (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) min_windspeed_below_canopy (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) minimum_cohort_size (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) minimum_mixing_depth (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) mix_and_ventilate() (in module virtual_ecosystem.models.abiotic.wind) mm_to_kg (virtual_ecosystem.core.model_config.CoreConstants attribute) model (virtual_ecosystem.core.registry.ModuleInfo attribute) model_classes (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) model_config_to_deflist() (in module virtual_ecosystem.core.docutils) model_config_to_html() (in module virtual_ecosystem.core.configuration) model_constant (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) model_constants (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.soil.pools.SoilPools attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) model_name (virtual_ecosystem.core.base_model.BaseDisturbance attribute) (virtual_ecosystem.core.base_model.BaseModel attribute)

model_post_init() (virtual_ecosystem.models.animal.model_config.AnimalConstants method) model_timing (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.core.core_components.CoreComponents attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) model_update_bounds (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) ModelConfigurationRoot (class in virtual_ecosystem.core.configuration) models (virtual_ecosystem.core.base_model.BaseDisturbance attribute) ModelTiming (class in virtual_ecosystem.core.core_components) module docstring_style virtual_ecosystem virtual_ecosystem.core virtual_ecosystem.core.axes virtual_ecosystem.core.base_model virtual_ecosystem.core.config_builder virtual_ecosystem.core.configuration virtual_ecosystem.core.core_components virtual_ecosystem.core.data virtual_ecosystem.core.docutils virtual_ecosystem.core.exceptions virtual_ecosystem.core.grid virtual_ecosystem.core.logger virtual_ecosystem.core.model_config virtual_ecosystem.core.readers virtual_ecosystem.core.registry virtual_ecosystem.core.utils virtual_ecosystem.core.variables virtual_ecosystem.entry_points virtual_ecosystem.example_data virtual_ecosystem.main virtual_ecosystem.models.abiotic virtual_ecosystem.models.abiotic.abiotic_model virtual_ecosystem.models.abiotic.abiotic_tools virtual_ecosystem.models.abiotic.energy_balance virtual_ecosystem.models.abiotic.microclimate virtual_ecosystem.models.abiotic.model_config virtual_ecosystem.models.abiotic.wind virtual_ecosystem.models.abiotic_simple virtual_ecosystem.models.abiotic_simple.abiotic_simple_model virtual_ecosystem.models.abiotic_simple.microclimate_simple virtual_ecosystem.models.abiotic_simple.model_config virtual_ecosystem.models.animal virtual_ecosystem.models.animal.animal_cohorts virtual_ecosystem.models.animal.animal_model virtual_ecosystem.models.animal.animal_traits virtual_ecosystem.models.animal.array_resources virtual_ecosystem.models.animal.cnp virtual_ecosystem.models.animal.decay virtual_ecosystem.models.animal.exporter virtual_ecosystem.models.animal.functional_group virtual_ecosystem.models.animal.model_config virtual_ecosystem.models.animal.protocols virtual_ecosystem.models.animal.scaling_functions virtual_ecosystem.models.hydrology virtual_ecosystem.models.hydrology.above_ground virtual_ecosystem.models.hydrology.below_ground virtual_ecosystem.models.hydrology.hydrology_model virtual_ecosystem.models.hydrology.hydrology_tools virtual_ecosystem.models.hydrology.model_config virtual_ecosystem.models.litter virtual_ecosystem.models.litter.carbon virtual_ecosystem.models.litter.chemistry virtual_ecosystem.models.litter.env_factors virtual_ecosystem.models.litter.inputs virtual_ecosystem.models.litter.litter_model virtual_ecosystem.models.litter.losses virtual_ecosystem.models.litter.model_config virtual_ecosystem.models.plants virtual_ecosystem.models.plants.biomasses virtual_ecosystem.models.plants.canopy virtual_ecosystem.models.plants.communities virtual_ecosystem.models.plants.exporter virtual_ecosystem.models.plants.functional_types virtual_ecosystem.models.plants.model_config virtual_ecosystem.models.plants.plants_model virtual_ecosystem.models.plants.subcanopy virtual_ecosystem.models.soil virtual_ecosystem.models.soil.env_factors virtual_ecosystem.models.soil.microbial_groups virtual_ecosystem.models.soil.model_config virtual_ecosystem.models.soil.pools virtual_ecosystem.models.soil.soil_model virtual_ecosystem.models.soil.uptake MODULE_REGISTRY (in module virtual_ecosystem.core.registry) ModuleInfo (class in virtual_ecosystem.core.registry) moisture_response_curvature (virtual_ecosystem.models.litter.model_config.LitterConstants attribute) molar_heat_capacity_air (virtual_ecosystem.core.model_config.CoreConstants attribute) molecular_weight_air (virtual_ecosystem.core.model_config.CoreConstants attribute) molecular_weight_ratio_water_to_dry_air (virtual_ecosystem.core.model_config.CoreConstants attribute) multiplier() (in module docstring_style) multiply_me() (docstring_style.MyClass method) myarg (docstring_style.MyClass attribute) myarg_multiple (docstring_style.MyClass attribute) MyClass (class in docstring_style)

N

n_canopy_layers (virtual_ecosystem.core.core_components.LayerStructure attribute) n_canopy_layers_filled (virtual_ecosystem.core.core_components.LayerStructure attribute) n_cells (virtual_ecosystem.core.core_components.LayerStructure attribute) n_layers (virtual_ecosystem.core.core_components.LayerStructure attribute) N_mineralisation_rate (virtual_ecosystem.models.litter.losses.LitterLosses attribute) N_sigma_opt_pred_prey (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) n_soil_layers (virtual_ecosystem.core.core_components.LayerStructure attribute) n_updates (virtual_ecosystem.core.core_components.ModelTiming attribute) name (docstring_style.MyClass attribute) (virtual_ecosystem.core.variables.VariableMetadata attribute) (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) (virtual_ecosystem.models.plants.biomasses.Element attribute) (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) ncells (virtual_ecosystem.core.grid.Grid attribute) necromass_decay_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) necromass_generation (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) necromass_n_flow (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) necromass_p_flow (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) necromass_sorption_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) neighbours (virtual_ecosystem.core.grid.Grid property) net_change_maom_bacteria (virtual_ecosystem.models.soil.pools.EnzymePoolChanges attribute) net_change_maom_fungi (virtual_ecosystem.models.soil.pools.EnzymePoolChanges attribute) net_change_pom_bacteria (virtual_ecosystem.models.soil.pools.EnzymePoolChanges attribute)

net_change_pom_fungi (virtual_ecosystem.models.soil.pools.EnzymePoolChanges attribute) NetNutrientConsumption (class in virtual_ecosystem.models.soil.uptake) new_amf_n_supply (virtual_ecosystem.models.soil.pools.PoolData attribute) new_amf_p_supply (virtual_ecosystem.models.soil.pools.PoolData attribute) new_emf_n_supply (virtual_ecosystem.models.soil.pools.PoolData attribute) new_emf_p_supply (virtual_ecosystem.models.soil.pools.PoolData attribute) new_fungal_fruiting_body_production (virtual_ecosystem.models.soil.pools.PoolData attribute) next_valid_above() (in module virtual_ecosystem.models.abiotic.wind) next_valid_below() (in module virtual_ecosystem.models.abiotic.wind) nitrate (virtual_ecosystem.models.soil.pools.WaterRemovalRates attribute) (virtual_ecosystem.models.soil.uptake.MaxUptakeRates attribute) (virtual_ecosystem.models.soil.uptake.NetNutrientConsumption attribute) nitrate_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) nitrification_maximum_temperature (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) nitrification_optimum_temperature (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) nitrification_rate_constant (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) nitrification_thermal_sensitivity (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) nitrogen_excreta_proportion (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) nitrogen_fixation_cost_equality_temperature (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) nitrogen_fixation_cost_infinite_temp_offset (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) nitrogen_fixation_cost_thermal_sensitivity (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) nitrogen_fixation_cost_zero_celcius (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) nitrogen_fixer_supply_fraction (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) nitrogen_fixers (virtual_ecosystem.models.soil.microbial_groups.CarbonSupply attribute) Nutrient (class in virtual_ecosystem.models.plants.subcanopy)

O

o_disp (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) occupancy_proportion (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) offspring_functional_group (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) on_core_axis() (virtual_ecosystem.core.data.Data method) organic_nitrogen (virtual_ecosystem.models.soil.uptake.MaxUptakeRates attribute) (virtual_ecosystem.models.soil.uptake.NetNutrientConsumption attribute) organic_phosphorus (virtual_ecosystem.models.soil.uptake.MaxUptakeRates attribute) (virtual_ecosystem.models.soil.uptake.NetNutrientConsumption attribute) organic_proportion_litter_nitrogen_leaching (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) organic_proportion_litter_phosphorus_leaching (virtual_ecosystem.models.soil.model_config.SoilConstants attribute)

out_continuous_file_name (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) out_final_file_name (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) out_folder_continuous (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) out_initial_file_name (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) out_merge_file_name (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) out_path (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) output_current_state() (virtual_ecosystem.core.data.Data method) output_directory (virtual_ecosystem.models.animal.exporter.AnimalCohortDataExporter attribute) (virtual_ecosystem.models.animal.exporter.ResourcePoolDataExporter attribute) (virtual_ecosystem.models.plants.exporter.CommunityDataExporter attribute)

P

p_above_t_max() (in module virtual_ecosystem.models.animal.scaling_functions) p_below_t_min() (in module virtual_ecosystem.models.animal.scaling_functions) P_mineralisation_rate (virtual_ecosystem.models.litter.losses.LitterLosses attribute) p_wet_dry (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.hydrology.model_config.HydrologyConfiguration attribute) p_wet_wet (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.hydrology.model_config.HydrologyConfiguration attribute) par_fraction_of_shortwave_radiation (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) parse() (virtual_ecosystem.models.animal.animal_traits.DietType class method) (virtual_ecosystem.models.animal.animal_traits.VerticalOccupancy class method) particulate_n (virtual_ecosystem.models.soil.pools.LitterMineralisationFluxes attribute) particulate_p (virtual_ecosystem.models.soil.pools.LitterMineralisationFluxes attribute) partion_plant_inputs_between_pools() (in module virtual_ecosystem.models.litter.inputs) partition_by_pft (virtual_ecosystem.models.animal.array_resources.ArrayResource attribute) (virtual_ecosystem.models.animal.array_resources.ArrayResourceDefinition attribute) per_propagule_annual_recruitment_probability (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) per_stem_annual_mortality_probability (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) per_stem_gpp (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) per_stem_transpiration (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) per_update_interval_stem_mortality_probability (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) permanent wilting point pft_definitions_path (virtual_ecosystem.models.plants.model_config.PlantsConfiguration attribute) pH (virtual_ecosystem.models.soil.env_factors.EnvironmentalEffectFactors attribute) phosphorus_deposition_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) placeholder (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSimpleConstants attribute) placeholder_annual_mean_temp (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) placeholder_annual_temp_sd (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) placeholder_validator() (in module virtual_ecosystem.core.configuration) plant_matter_type (virtual_ecosystem.models.animal.decay.HerbivoryWaste attribute) plant_reproductive_tissue_lignin (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) PlantCommunities (class in virtual_ecosystem.models.plants.communities) PlantsConfiguration (class in virtual_ecosystem.models.plants.model_config) PlantsConstants (class in virtual_ecosystem.models.plants.model_config) PlantsExportConfig (class in virtual_ecosystem.models.plants.model_config) PlantsModel (class in virtual_ecosystem.models.plants.plants_model)

pmodel (virtual_ecosystem.core.model_config.PyrealmConfig attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) polygons (virtual_ecosystem.core.grid.Grid attribute) POM pom (virtual_ecosystem.models.soil.pools.LitterMineralisationFluxes attribute) pom_enzyme_bacteria_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) pom_enzyme_fungi_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) pom_to_lmwc (virtual_ecosystem.models.soil.pools.EnzymeMediatedRates attribute) Pool (class in virtual_ecosystem.models.animal.protocols) pool_array (virtual_ecosystem.models.animal.array_resources.ArrayResource attribute) (virtual_ecosystem.models.animal.array_resources.ArrayResourceDefinition attribute) PoolData (class in virtual_ecosystem.models.soil.pools) pools (virtual_ecosystem.models.soil.pools.SoilPools attribute) populate_distances() (virtual_ecosystem.core.grid.Grid method) populate_fungal_fruiting_bodies() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) populate_soil_pools() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) population_density_terms (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) pore_connectivity_parameter (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) potential_evaporation_leaf() (in module virtual_ecosystem.models.hydrology.above_ground) prepare_static_inputs() (in module virtual_ecosystem.models.abiotic.microclimate) prey_group_selection() (in module virtual_ecosystem.models.animal.scaling_functions) prey_groups (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) prey_mass_scaling_terms (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) prey_scaling (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) primary_phosphorus_breakdown_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) priority (virtual_ecosystem.core.configuration.DisturbanceConfigurationRoot attribute) Progress (class in virtual_ecosystem.main) propagule_mass_portion (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) pyrealm (virtual_ecosystem.core.model_config.CoreConfiguration attribute) pyrealm_core_constants (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) pyrealm_core_consts (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) pyrealm_pmodel_consts (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) PyrealmConfig (class in virtual_ecosystem.core.model_config)

R

rainfall_scale_parameter (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.hydrology.model_config.HydrologyConfiguration attribute) rainfall_shape_parameter (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.hydrology.model_config.HydrologyConfiguration attribute) raw_biomass_density_kg_m2() (in module virtual_ecosystem.models.animal.scaling_functions) reconciled_run_length (virtual_ecosystem.core.core_components.ModelTiming attribute) record_hourly_output() (in module virtual_ecosystem.models.abiotic.abiotic_tools) record_trophic_transfer() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) reference_cue_logit (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) reference_temperature (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) refreshed_variables (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) register_disturbance() (in module virtual_ecosystem.core.registry) register_file_format_loader() (in module virtual_ecosystem.core.readers) register_grid() (in module virtual_ecosystem.core.grid) register_module() (in module virtual_ecosystem.core.registry) reintegrate_cohort() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) reintegrate_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) related_models (virtual_ecosystem.core.variables.VariableMetadata property) relative soil moisture relative_humidity (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSimpleBounds attribute) remaining_time_away (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) remove_dead_cohort() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) remove_dead_cohort_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) remove_file_logger() (in module virtual_ecosystem.core.logger) remove_mass_fraction() (virtual_ecosystem.models.plants.subcanopy.SubcanopyBiomass method) reproductive_allocation (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) reproductive_environment (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) reproductive_mass (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort property) reproductive_mass_cnp (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) reproductive_type (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) ReproductiveBiomass (class in virtual_ecosystem.models.plants.biomasses) ReproductiveEnvironment (class in virtual_ecosystem.models.animal.animal_traits) ReproductiveType (class in virtual_ecosystem.models.animal.animal_traits) required_attributes (virtual_ecosystem.models.animal.exporter.AnimalCohortDataExporter attribute) required_data (virtual_ecosystem.models.plants.exporter.CommunityDataExporter attribute) (virtual_ecosystem.models.plants.model_config.PlantsExportConfig attribute) REQUIRED_ENZYMES (in module virtual_ecosystem.models.soil.model_config) REQUIRED_MICROBIAL_GROUPS (in module virtual_ecosystem.models.soil.model_config)

reservoir_const_lower_groundwater (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) reservoir_const_upper_groundwater (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) reset() (virtual_ecosystem.models.animal.decay.CarcassPool method) (virtual_ecosystem.models.animal.decay.ExcrementPool method) reset_trophic_record() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) reset_trophic_records() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) reset_update_vars() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) Resource (class in virtual_ecosystem.models.animal.protocols) resource (virtual_ecosystem.models.animal.array_resources.CellResource attribute) resource_pool_exporter (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) ResourcePool (class in virtual_ecosystem.models.animal.array_resources) ResourcePoolDataExporter (class in virtual_ecosystem.models.animal.exporter) ResourcePoolExportConfig (class in virtual_ecosystem.models.animal.model_config) respire() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) river discharge rate root_exudates (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) root_lignin (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) root_mass (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) RootBiomass (class in virtual_ecosystem.models.plants.biomasses) roots_meta_split (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) roughness_element_drag_coefficient (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) roughness_sublayer_depth_parameter (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) route_horizontal_flow() (in module virtual_ecosystem.models.hydrology.above_ground) RST_TO_MD (in module virtual_ecosystem.core.configuration) (in module virtual_ecosystem.core.docutils) run_at (virtual_ecosystem.core.configuration.DisturbanceConfigurationRoot attribute) run_every (virtual_ecosystem.core.configuration.DisturbanceConfigurationRoot attribute) run_hour_step() (in module virtual_ecosystem.models.abiotic.microclimate) run_length (virtual_ecosystem.core.core_components.ModelTiming attribute) (virtual_ecosystem.core.model_config.TimingConfiguration attribute) run_length_quantity (virtual_ecosystem.core.core_components.ModelTiming attribute) run_length_seconds (virtual_ecosystem.core.model_config.TimingConfiguration property) run_microclimate() (in module virtual_ecosystem.models.abiotic.microclimate) run_simple_microclimate() (in module virtual_ecosystem.models.abiotic_simple.microclimate_simple) run_validation() (virtual_ecosystem.core.axes.AxisValidator method) (virtual_ecosystem.core.axes.Spat_CellId_Coord_Any method) (virtual_ecosystem.core.axes.Spat_CellId_Dim_Any method) (virtual_ecosystem.core.axes.Spat_XY_Coord_Square method) (virtual_ecosystem.core.axes.Spat_XY_Dim_Square method) (virtual_ecosystem.core.axes.Time method)

S

saprotrophic_fungi (virtual_ecosystem.models.soil.pools.BiomassLosses attribute) saprotrophic_fungi_change (virtual_ecosystem.models.soil.pools.MicrobialChanges attribute) saturated_hydraulic_conductivity (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) saturated_pressure_slope_parameters (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) save_continuous_data (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) save_final_state (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) save_initial_state (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) save_merged_config (virtual_ecosystem.core.model_config.DataOutputConfiguration attribute) save_timeslice_to_netcdf() (virtual_ecosystem.core.data.Data method) save_to_netcdf() (virtual_ecosystem.core.data.Data method) scavengeable_cnp (virtual_ecosystem.models.animal.decay.CarcassPool attribute) (virtual_ecosystem.models.animal.decay.ExcrementPool attribute) ScavengeableMixin (class in virtual_ecosystem.models.animal.decay) ScavengeableResource (class in virtual_ecosystem.models.animal.protocols) scavenging_rate_carcasses (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) scavenging_rate_excrement (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) seasonal_migration_probability (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) secant_solve_cells_layers() (in module virtual_ecosystem.models.abiotic.energy_balance) secondary_phosphorus_breakdown_rate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) seconds_to_day (virtual_ecosystem.core.model_config.CoreConstants attribute) seconds_to_hour (virtual_ecosystem.core.model_config.CoreConstants attribute) SeedBiomass (class in virtual_ecosystem.models.plants.biomasses) semelparity_mass_loss (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) senesced_leaf_lignin (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) senescence_mortality() (in module virtual_ecosystem.models.animal.scaling_functions) serialise_diet_type() (in module virtual_ecosystem.models.animal.model_config) set_canopy_top_radiation() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) set_filled_canopy() (virtual_ecosystem.core.core_components.LayerStructure method) set_light_capture() (virtual_ecosystem.models.plants.subcanopy.Subcanopy method) set_neighbours() (virtual_ecosystem.core.grid.Grid method) set_resources() (virtual_ecosystem.models.animal.array_resources.ResourcePool method) set_shortwave_absorption() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) set_unintended_nan_to_zero() (in module virtual_ecosystem.models.abiotic.abiotic_tools) setup_hydrology_input_current_timestep() (in module virtual_ecosystem.models.hydrology.hydrology_tools) setup_variables() (in module virtual_ecosystem.core.variables) sigma_f_t (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) sigma_opt_f (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) sigma_opt_pred_prey (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) simple_constants (virtual_ecosystem.models.abiotic.model_config.AbioticConfiguration attribute) small_perturbation_second_guess_secant_solver (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) soil matric potential soil moisture soil moisture at field capacity soil moisture capacity soil moisture residual soil moisture saturation soil_c_pool_arbuscular_mycorrhiza (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_c_pool_bacteria (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_c_pool_ectomycorrhiza (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_c_pool_saprotrophic_fungi (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_lmwc_carbon (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_lmwc_nitrogen (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_lmwc_phosphorus (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_maom_carbon (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_maom_nitrogen (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_maom_phosphorus (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_necromass_carbon (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_necromass_nitrogen (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_necromass_phosphorus (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_pom_carbon (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_pom_nitrogen (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_cnp_pool_pom_phosphorus (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_emissivity (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSharedConstants attribute) (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSimpleConstants attribute) soil_enzyme_maom_bacteria (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_enzyme_maom_fungi (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_enzyme_pom_bacteria (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_enzyme_pom_fungi (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_layer_active_thickness (virtual_ecosystem.core.core_components.LayerStructure attribute) soil_layer_depths (virtual_ecosystem.core.core_components.LayerStructure attribute) soil_layer_thickness (virtual_ecosystem.core.core_components.LayerStructure attribute) soil_layer_thickness_mm (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) soil_layers (virtual_ecosystem.core.model_config.LayersConfiguration attribute) soil_microbe_water_potential_halt (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) soil_microbe_water_potential_optimum (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) soil_moisture_residual (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) soil_moisture_saturation (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) soil_n_pool_ammonium (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_n_pool_nitrate (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_p_pool_labile (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_p_pool_primary (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_p_pool_secondary (virtual_ecosystem.models.soil.pools.PoolData attribute) soil_pools (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute)

soil_protection_with_clay (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) soil_temperature (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSimpleBounds attribute) soil_thermal_conductivity (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) SoilConfiguration (class in virtual_ecosystem.models.soil.model_config) SoilConstants (class in virtual_ecosystem.models.soil.model_config) SoilEnzymeClass (class in virtual_ecosystem.models.soil.model_config) SoilMicrobialGroup (class in virtual_ecosystem.models.soil.model_config) SoilModel (class in virtual_ecosystem.models.soil.soil_model) SoilPool (class in virtual_ecosystem.models.animal.decay) SoilPools (class in virtual_ecosystem.models.soil.pools) solubility_coefficient_ammonium (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) solubility_coefficient_labile_p (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) solubility_coefficient_lmwc (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) solubility_coefficient_nitrate (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) sort_disturbances() (in module virtual_ecosystem.main) source (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) Spat_CellId_Coord_Any (class in virtual_ecosystem.core.axes) Spat_CellId_Dim_Any (class in virtual_ecosystem.core.axes) Spat_XY_Coord_Square (class in virtual_ecosystem.core.axes) Spat_XY_Dim_Square (class in virtual_ecosystem.core.axes) specific soil moisture specific_gas_constant_dry_air (virtual_ecosystem.core.model_config.CoreConstants attribute) specific_heat_capacity_soil (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) spinup() (virtual_ecosystem.core.base_model.BaseModel method) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel method) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel method) (virtual_ecosystem.models.animal.animal_model.AnimalModel method) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel method) (virtual_ecosystem.models.litter.litter_model.LitterModel method) (virtual_ecosystem.models.plants.plants_model.PlantsModel method) (virtual_ecosystem.models.soil.soil_model.SoilModel method) split_arrays_by_grouping_variable() (in module virtual_ecosystem.core.utils) split_pool_into_metabolic_and_structural_litter() (in module virtual_ecosystem.models.litter.inputs) standard_mole (virtual_ecosystem.core.model_config.CoreConstants attribute) standard_pressure (virtual_ecosystem.core.model_config.CoreConstants attribute) start_date (virtual_ecosystem.core.model_config.TimingConfiguration attribute) start_time (virtual_ecosystem.core.core_components.ModelTiming attribute) starvation_mortality() (in module virtual_ecosystem.models.animal.scaling_functions) static (virtual_ecosystem.core.configuration.ModelConfigurationRoot attribute) (virtual_ecosystem.models.abiotic.model_config.AbioticConfiguration attribute) (virtual_ecosystem.models.animal.model_config.AnimalConfiguration attribute) (virtual_ecosystem.models.hydrology.model_config.HydrologyConfiguration attribute) (virtual_ecosystem.models.litter.model_config.LitterConfiguration attribute) (virtual_ecosystem.models.plants.model_config.PlantsConfiguration attribute) (virtual_ecosystem.models.soil.model_config.SoilConfiguration attribute) stefan_boltzmann_constant (virtual_ecosystem.core.model_config.CoreConstants attribute) stem_allocations (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) stem_canopy_attributes (virtual_ecosystem.models.plants.exporter.CommunityDataExporter attribute) (virtual_ecosystem.models.plants.model_config.PlantsExportConfig attribute) stem_lignin (virtual_ecosystem.models.litter.inputs.LitterInputs attribute) (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) StemBiomass (class in virtual_ecosystem.models.plants.biomasses) sub-surface runoff Subcanopy (class in virtual_ecosystem.models.plants.subcanopy) subcanopy (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) subcanopy_extinction_coef (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_layer_height (virtual_ecosystem.core.model_config.LayersConfiguration attribute) subcanopy_reproductive_allocation (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_respiration_fraction (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_seedbank_c_n_ratio (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_seedbank_c_p_ratio (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_seedbank_lignin (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_seedbank_turnover (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_specific_leaf_area (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_sprout_rate (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_sprout_yield (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_vegetation_c_n_ratio (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_vegetation_c_p_ratio (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_vegetation_lignin (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_vegetation_turnover (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) subcanopy_yield (virtual_ecosystem.models.plants.model_config.PlantsConstants attribute) SubcanopyBiomass (class in virtual_ecosystem.models.plants.subcanopy) substrate (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) substrate_surface_roughness_length (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) SUBSTRATES (in module virtual_ecosystem.models.soil.model_config) surface runoff surface_albedo (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) surface_layer_height (virtual_ecosystem.core.core_components.LayerStructure attribute) (virtual_ecosystem.core.model_config.LayersConfiguration attribute) surface_layer_index (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) symbiote_nitrogen_uptake_fraction (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) symbiote_phosphorus_uptake_fraction (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) synthesis_nutrient_ratios (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute)

T

T (class in virtual_ecosystem.core.configuration) t_max_crit (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) t_max_crit_ectotherm() (in module virtual_ecosystem.models.animal.scaling_functions) t_min_crit (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) t_min_crit_ectotherm() (in module virtual_ecosystem.models.animal.scaling_functions) t_opt (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) t_opt_ectotherm() (in module virtual_ecosystem.models.animal.scaling_functions) target_cohorts_per_fg (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) tau_f (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) taxa (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) TaxaType (class in virtual_ecosystem.models.animal.animal_traits) taxonomic_group (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) tectonic_uplift_rate_phosphorus (virtual_ecosystem.models.soil.model_config.SoilConstants attribute) territory (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) territory_cells (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) territory_size (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) territory_size() (in module virtual_ecosystem.models.animal.scaling_functions) territory_size_terms (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) theta_i_j() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) theta_opt_f (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) theta_opt_i() (in module virtual_ecosystem.models.animal.scaling_functions) theta_opt_min_f (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) Time (class in virtual_ecosystem.core.axes) time_since_maturity (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) time_to_maturity (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) timing (virtual_ecosystem.core.base_model.BaseDisturbance attribute) (virtual_ecosystem.core.model_config.CoreConfiguration attribute)

timing_options_are_not_both_empty() (virtual_ecosystem.core.configuration.DisturbanceConfigurationRoot method) TimingConfiguration (class in virtual_ecosystem.core.model_config) tissue_deficit (virtual_ecosystem.models.plants.biomasses.Biomasses property) tissue_name (virtual_ecosystem.models.plants.biomasses.BiomassTissueABC attribute) (virtual_ecosystem.models.plants.biomasses.FoliageBiomass attribute) (virtual_ecosystem.models.plants.biomasses.FruitBiomass attribute) (virtual_ecosystem.models.plants.biomasses.ReproductiveBiomass attribute) (virtual_ecosystem.models.plants.biomasses.RootBiomass attribute) (virtual_ecosystem.models.plants.biomasses.SeedBiomass attribute) (virtual_ecosystem.models.plants.biomasses.StemBiomass attribute) tissue_names (virtual_ecosystem.models.plants.biomasses.Biomasses attribute) tissues (virtual_ecosystem.models.plants.biomasses.Biomasses attribute) to_camel_case() (in module virtual_ecosystem.core.base_model) to_per_day() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) to_per_volume() (virtual_ecosystem.models.soil.pools.SoilPools method) to_total_mass() (virtual_ecosystem.models.soil.soil_model.SoilModel method) toml_contents (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) toml_files (virtual_ecosystem.core.config_builder.ConfigurationLoader attribute) total (virtual_ecosystem.models.animal.cnp.CNP property) total runoff total_element_masses (virtual_ecosystem.models.plants.biomasses.Biomasses property) total_heterotroph_biomass_density_kg_m2 (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) trophic_record (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort attribute) truncate_run_at_update (virtual_ecosystem.core.model_config.DebugConfiguration attribute) turnover_rate (virtual_ecosystem.models.soil.microbial_groups.MicrobialGroupConstants attribute) (virtual_ecosystem.models.soil.model_config.SoilEnzymeClass attribute) (virtual_ecosystem.models.soil.model_config.SoilMicrobialGroup attribute) turnover_ratio (virtual_ecosystem.models.plants.biomasses.Element attribute)

U

u_bg (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) understorey_ventilation_rate (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) unique_axes() (virtual_ecosystem.core.variables.VariableMetadata class method) unit (virtual_ecosystem.core.variables.VariableMetadata attribute) update() (virtual_ecosystem.core.base_model.BaseModel method) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel method) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel method) (virtual_ecosystem.models.animal.animal_model.AnimalModel method) (virtual_ecosystem.models.animal.cnp.CNP method) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel method) (virtual_ecosystem.models.litter.litter_model.LitterModel method) (virtual_ecosystem.models.plants.plants_model.PlantsModel method) (virtual_ecosystem.models.soil.soil_model.SoilModel method) update_activity_window() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) update_activity_windows_community() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) update_air_temperature() (in module virtual_ecosystem.models.abiotic.microclimate) update_allometry() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) update_atmospheric_humidity() (in module virtual_ecosystem.models.abiotic.microclimate) update_canopy_air_temperature() (in module virtual_ecosystem.models.abiotic.energy_balance) update_canopy_layers() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) update_carcass_pool() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) update_cohort_bookkeeping() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) update_community_bookkeeping() (virtual_ecosystem.models.animal.animal_model.AnimalModel method)

update_community_occupancy() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) update_datestamps (virtual_ecosystem.core.core_components.ModelTiming attribute) update_forcing_boundary_conditions() (in module virtual_ecosystem.models.abiotic.microclimate) update_fungal_fruiting_bodies() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) update_fungal_fruiting_bodies_in_data() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) update_groundwater_storage() (in module virtual_ecosystem.models.hydrology.below_ground) update_humidity_vpd() (in module virtual_ecosystem.models.abiotic.energy_balance) update_interval (virtual_ecosystem.core.core_components.ModelTiming attribute) (virtual_ecosystem.core.model_config.TimingConfiguration attribute) update_interval_quantity (virtual_ecosystem.core.core_components.ModelTiming attribute) update_interval_seconds (virtual_ecosystem.core.core_components.ModelTiming attribute) (virtual_ecosystem.core.model_config.TimingConfiguration property) update_interval_timedelta (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) update_largest_mass() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) update_migrated_and_aquatic() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) update_population_densities() (virtual_ecosystem.models.animal.animal_model.AnimalModel method) update_profile_from_reference() (in module virtual_ecosystem.models.abiotic.abiotic_tools) update_soil_moisture() (in module virtual_ecosystem.models.hydrology.below_ground) update_soil_temperature() (in module virtual_ecosystem.models.abiotic.energy_balance) update_specific_humidity() (in module virtual_ecosystem.models.abiotic.energy_balance) update_surface_air_temperature() (in module virtual_ecosystem.models.abiotic.energy_balance) update_territory() (virtual_ecosystem.models.animal.animal_cohorts.AnimalCohort method) updates_per_year (virtual_ecosystem.core.core_components.ModelTiming attribute)

V

V_disp (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute) validate_dataarray() (in module virtual_ecosystem.core.axes) validate_variables() (in module virtual_ecosystem.models.abiotic.abiotic_tools) van_genuchten_nonlinearily_parameter (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) vapour_pressure_deficit (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSimpleBounds attribute) variable_table() (in module virtual_ecosystem.core.docutils) variable_type (virtual_ecosystem.core.variables.VariableMetadata attribute) variable_validation (virtual_ecosystem.core.data.Data attribute) VariableMetadata (class in virtual_ecosystem.core.variables) VariablesFile (class in virtual_ecosystem.core.variables) vars_populated_by_first_update (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.core.variables.VariableMetadata attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) vars_populated_by_init (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.core.variables.VariableMetadata attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) vars_required_by_init (virtual_ecosystem.core.variables.VariableMetadata attribute) vars_required_by_update (virtual_ecosystem.core.variables.VariableMetadata attribute) vars_required_for_init (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) vars_required_for_update (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) vars_updated (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.core.variables.VariableMetadata attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animal.animal_model.AnimalModel attribute) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) ve_run() (in module virtual_ecosystem.main) ve_run_cli() (in module virtual_ecosystem.entry_points) veg_density_param (virtual_ecosystem.models.hydrology.model_config.HydrologyConstants attribute) vertical_occupancy (virtual_ecosystem.models.animal.array_resources.ArrayResource attribute) (virtual_ecosystem.models.animal.array_resources.ArrayResourceDefinition attribute) (virtual_ecosystem.models.animal.decay.CarcassPool attribute) (virtual_ecosystem.models.animal.decay.ExcrementPool attribute) (virtual_ecosystem.models.animal.decay.FungalFruitPool attribute) (virtual_ecosystem.models.animal.decay.SoilPool attribute) (virtual_ecosystem.models.animal.functional_group.FunctionalGroup attribute) VerticalOccupancy (class in virtual_ecosystem.models.animal.animal_traits) virtual_ecosystem module virtual_ecosystem.core module virtual_ecosystem.core.axes module virtual_ecosystem.core.base_model module virtual_ecosystem.core.config_builder module virtual_ecosystem.core.configuration module virtual_ecosystem.core.core_components module virtual_ecosystem.core.data module virtual_ecosystem.core.docutils module virtual_ecosystem.core.exceptions module virtual_ecosystem.core.grid module virtual_ecosystem.core.logger module virtual_ecosystem.core.model_config module virtual_ecosystem.core.readers module virtual_ecosystem.core.registry module virtual_ecosystem.core.utils module virtual_ecosystem.core.variables module virtual_ecosystem.entry_points module virtual_ecosystem.example_data module virtual_ecosystem.main module

virtual_ecosystem.models.abiotic module virtual_ecosystem.models.abiotic.abiotic_model module virtual_ecosystem.models.abiotic.abiotic_tools module virtual_ecosystem.models.abiotic.energy_balance module virtual_ecosystem.models.abiotic.microclimate module virtual_ecosystem.models.abiotic.model_config module virtual_ecosystem.models.abiotic.wind module virtual_ecosystem.models.abiotic_simple module virtual_ecosystem.models.abiotic_simple.abiotic_simple_model module virtual_ecosystem.models.abiotic_simple.microclimate_simple module virtual_ecosystem.models.abiotic_simple.model_config module virtual_ecosystem.models.animal module virtual_ecosystem.models.animal.animal_cohorts module virtual_ecosystem.models.animal.animal_model module virtual_ecosystem.models.animal.animal_traits module virtual_ecosystem.models.animal.array_resources module virtual_ecosystem.models.animal.cnp module virtual_ecosystem.models.animal.decay module virtual_ecosystem.models.animal.exporter module virtual_ecosystem.models.animal.functional_group module virtual_ecosystem.models.animal.model_config module virtual_ecosystem.models.animal.protocols module virtual_ecosystem.models.animal.scaling_functions module virtual_ecosystem.models.hydrology module virtual_ecosystem.models.hydrology.above_ground module virtual_ecosystem.models.hydrology.below_ground module virtual_ecosystem.models.hydrology.hydrology_model module virtual_ecosystem.models.hydrology.hydrology_tools module virtual_ecosystem.models.hydrology.model_config module virtual_ecosystem.models.litter module virtual_ecosystem.models.litter.carbon module virtual_ecosystem.models.litter.chemistry module virtual_ecosystem.models.litter.env_factors module virtual_ecosystem.models.litter.inputs module virtual_ecosystem.models.litter.litter_model module virtual_ecosystem.models.litter.losses module virtual_ecosystem.models.litter.model_config module virtual_ecosystem.models.plants module virtual_ecosystem.models.plants.biomasses module virtual_ecosystem.models.plants.canopy module virtual_ecosystem.models.plants.communities module virtual_ecosystem.models.plants.exporter module virtual_ecosystem.models.plants.functional_types module virtual_ecosystem.models.plants.model_config module virtual_ecosystem.models.plants.plants_model module virtual_ecosystem.models.plants.subcanopy module virtual_ecosystem.models.soil module virtual_ecosystem.models.soil.env_factors module virtual_ecosystem.models.soil.microbial_groups module virtual_ecosystem.models.soil.model_config module virtual_ecosystem.models.soil.pools module virtual_ecosystem.models.soil.soil_model module virtual_ecosystem.models.soil.uptake module von_karmans_constant (virtual_ecosystem.core.model_config.CoreConstants attribute)

W

w_bar_i_j() (in module virtual_ecosystem.models.animal.scaling_functions) water (virtual_ecosystem.models.soil.env_factors.EnvironmentalEffectFactors attribute) WaterRemovalRates (class in virtual_ecosystem.models.soil.pools) wind_reference_height (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) wind_speed (virtual_ecosystem.models.abiotic_simple.model_config.AbioticSimpleBounds attribute) with_traceback() (virtual_ecosystem.models.soil.soil_model.IntegrationError method) woody (virtual_ecosystem.models.litter.inputs.LitterInputs attribute)

woody_carbon (virtual_ecosystem.models.litter.losses.LitterLosses attribute) woody_lignin (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) woody_nitrogen (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) woody_phosphorus (virtual_ecosystem.models.litter.inputs.InputChemistries attribute) (virtual_ecosystem.models.litter.losses.LitterLosses attribute) write_consumption() (virtual_ecosystem.models.animal.array_resources.ResourcePool method)

X

xoff (virtual_ecosystem.core.grid.Grid attribute) (virtual_ecosystem.core.model_config.GridConfiguration attribute)

Y

yoff (virtual_ecosystem.core.grid.Grid attribute) (virtual_ecosystem.core.model_config.GridConfiguration attribute)

Z

zero_Celsius (virtual_ecosystem.core.model_config.CoreConstants attribute)

zero_plane_scaling_parameter (virtual_ecosystem.models.abiotic.model_config.AbioticConstants attribute) zeta_st (virtual_ecosystem.models.animal.model_config.AnimalConstants attribute)