Index

_

__contains__() (virtual_ecosystem.core.data.Data method) __getitem__() (virtual_ecosystem.core.data.Data method) __init__() (virtual_ecosystem.core.base_model.BaseModel method) (virtual_ecosystem.models.abiotic.constants.AbioticConsts method) (virtual_ecosystem.models.abiotic_simple.constants.AbioticSimpleBounds method) (virtual_ecosystem.models.abiotic_simple.constants.AbioticSimpleConsts method) (virtual_ecosystem.models.hydrology.constants.HydroConsts method) __init_subclass__() (virtual_ecosystem.core.axes.AxisValidator 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.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.BaseModel class method) _check_model_update_bounds() (virtual_ecosystem.core.base_model.BaseModel class method) _check_required_init_vars() (virtual_ecosystem.core.base_model.BaseModel class method) _check_vars_updated() (virtual_ecosystem.core.base_model.BaseModel class method) _parse_command_line_params() (in module virtual_ecosystem.entry_points) _parse_param_str() (in module virtual_ecosystem.entry_points)

A

a_class_attribute (docstring_style.MyClass attribute) AbioticConsts (class in virtual_ecosystem.models.abiotic.constants) AbioticModel (class in virtual_ecosystem.models.abiotic.abiotic_model) AbioticSimpleBounds (class in virtual_ecosystem.models.abiotic_simple.constants) AbioticSimpleConsts (class in virtual_ecosystem.models.abiotic_simple.constants) AbioticSimpleModel (class in virtual_ecosystem.models.abiotic_simple.abiotic_simple_model) above_canopy_height_offset (virtual_ecosystem.core.core_components.LayerStructure attribute) accumulate_horizontal_flow() (in module virtual_ecosystem.models.hydrology.above_ground) activation_energy_labile_C_saturation (virtual_ecosystem.models.soil.constants.SoilConsts attribute) activation_energy_maom_decomp_rate (virtual_ecosystem.models.soil.constants.SoilConsts attribute) activation_energy_maom_decomp_saturation (virtual_ecosystem.models.soil.constants.SoilConsts attribute) activation_energy_microbial_turnover (virtual_ecosystem.models.soil.constants.SoilConsts attribute) activation_energy_microbial_uptake (virtual_ecosystem.models.soil.constants.SoilConsts attribute) activation_energy_pom_decomp_rate (virtual_ecosystem.models.soil.constants.SoilConsts attribute) activation_energy_pom_decomp_saturation (virtual_ecosystem.models.soil.constants.SoilConsts attribute) add_file_logger() (in module virtual_ecosystem.core.logger) add_from_dict() (virtual_ecosystem.core.data.Data method) adult_mass (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute)

adult_natural_mortality_prob (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) age (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) air_entry_water_potential (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) air_temperature (virtual_ecosystem.models.abiotic_simple.constants.AbioticSimpleBounds attribute) all_animal_cohorts (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity property) allocate_gpp() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) alpha_0_herb (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) alpha_0_pred (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) alpha_i_j() (in module virtual_ecosystem.models.animals.scaling_functions) alpha_i_k() (in module virtual_ecosystem.models.animals.scaling_functions) AN_OBJECT (in module docstring_style) animal_cohorts (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity attribute) AnimalCohort (class in virtual_ecosystem.models.animals.animal_cohorts) AnimalCommunity (class in virtual_ecosystem.models.animals.animal_communities) AnimalConsts (class in virtual_ecosystem.models.animals.constants) AnimalModel (class in virtual_ecosystem.models.animals.animal_model) arrhenius_reference_temp (virtual_ecosystem.models.soil.constants.SoilConsts attribute) AXIS_VALIDATORS (in module virtual_ecosystem.core.axes) AxisValidator (class in virtual_ecosystem.core.axes)

B

b_herb (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) b_pred (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) base_soil_protection (virtual_ecosystem.models.soil.constants.SoilConsts attribute) BaseModel (class in virtual_ecosystem.core.base_model) beta_responsive_bodymass (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) birth() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) birth_community() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method)

birth_mass (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) bottom_leaf_air_conductivity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) bottom_leaf_vapour_conductivity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) bounds (virtual_ecosystem.core.grid.Grid attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) build_canopy_arrays() (in module virtual_ecosystem.models.plants.canopy) build_config() (virtual_ecosystem.core.config.Config method) build_schema() (virtual_ecosystem.core.config.Config method)

C

c_tol (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) c_tsm (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) calculate_air_heat_conductivity_above() (in module virtual_ecosystem.models.abiotic.conductivities) calculate_air_heat_conductivity_canopy() (in module virtual_ecosystem.models.abiotic.conductivities) calculate_alpha() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_bypass_flow() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_carbon_mineralised() (in module virtual_ecosystem.models.litter.litter_pools) calculate_carbon_use_efficiency() (in module virtual_ecosystem.models.soil.carbon) calculate_change_in_lignin() (in module virtual_ecosystem.models.litter.litter_pools) calculate_change_in_litter_variables() (in module virtual_ecosystem.models.litter.litter_pools) calculate_clay_impact_on_enzyme_saturation() (in module virtual_ecosystem.models.soil.env_factors) calculate_clay_impact_on_necromass_decay() (in module virtual_ecosystem.models.soil.env_factors) calculate_consumed_mass_herbivory() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_consumed_mass_predation() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_current_conductivities() (in module virtual_ecosystem.models.abiotic.conductivities) calculate_decay_rates() (in module virtual_ecosystem.models.litter.litter_pools) calculate_delta_canopy_temperature() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_density_for_cohort() (virtual_ecosystem.models.animals.animal_model.AnimalModel method) calculate_diabatic_correction_above() (in module virtual_ecosystem.models.abiotic.wind) calculate_diabatic_correction_canopy() (in module virtual_ecosystem.models.abiotic.wind) calculate_drainage_map() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_environmental_effect_factors() (in module virtual_ecosystem.models.soil.env_factors) calculate_environmental_factors() (in module virtual_ecosystem.models.litter.litter_pools) calculate_enzyme_mediated_decomposition() (in module virtual_ecosystem.models.soil.carbon) calculate_enzyme_turnover() (in module virtual_ecosystem.models.soil.carbon) calculate_friction_velocity_reference_height() (in module virtual_ecosystem.models.abiotic.wind) calculate_ground_heat_flux() (in module virtual_ecosystem.models.abiotic.soil_energy_balance) calculate_interception() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_latent_heat_flux_from_soil_evaporation() (in module virtual_ecosystem.models.abiotic.soil_energy_balance) calculate_latent_heat_vapourisation() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_leaching_rate() (in module virtual_ecosystem.models.soil.env_factors) calculate_leaf_air_heat_conductivity() (in module virtual_ecosystem.models.abiotic.conductivities) calculate_leaf_and_air_temperature() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_leaf_vapour_conductivity() (in module virtual_ecosystem.models.abiotic.conductivities) calculate_lignin_updates() (in module virtual_ecosystem.models.litter.litter_pools) calculate_litter_additions() (virtual_ecosystem.models.animals.animal_model.AnimalModel method) calculate_litter_chemistry_factor() (in module virtual_ecosystem.models.litter.litter_pools) calculate_litter_decay_metabolic_above() (in module virtual_ecosystem.models.litter.litter_pools) calculate_litter_decay_metabolic_below() (in module virtual_ecosystem.models.litter.litter_pools) calculate_litter_decay_structural_above() (in module virtual_ecosystem.models.litter.litter_pools) calculate_litter_decay_structural_below() (in module virtual_ecosystem.models.litter.litter_pools) calculate_litter_decay_woody() (in module virtual_ecosystem.models.litter.litter_pools) calculate_longwave_emission() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_maintenance_biomass_synthesis() (in module virtual_ecosystem.models.soil.carbon) calculate_mean_mixing_length() (in module virtual_ecosystem.models.abiotic.wind) calculate_microbial_carbon_uptake() (in module virtual_ecosystem.models.soil.carbon) calculate_moisture_effect_on_litter_decomp() (in module virtual_ecosystem.models.litter.litter_pools) calculate_molar_density_air() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_pH_suitability() (in module virtual_ecosystem.models.soil.env_factors) calculate_potential_consumed_biomass() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_potential_prey_consumed() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_predation_search_rate() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_predation_success_probability() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_roughness_length_momentum() (in module virtual_ecosystem.models.abiotic.wind) calculate_saturation_vapour_pressure() (in module virtual_ecosystem.models.abiotic_simple.microclimate) calculate_sensible_heat_flux_soil() (in module virtual_ecosystem.models.abiotic.soil_energy_balance) calculate_slope_of_saturated_pressure_curve() (in module virtual_ecosystem.models.abiotic.energy_balance) calculate_soil_absorption() (in module virtual_ecosystem.models.abiotic.soil_energy_balance) calculate_soil_carbon_updates() (in module virtual_ecosystem.models.soil.carbon) calculate_soil_evaporation() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_soil_heat_balance() (in module virtual_ecosystem.models.abiotic.soil_energy_balance) calculate_specific_heat_air() (in module virtual_ecosystem.models.abiotic.abiotic_tools) calculate_surface_runoff() (in module virtual_ecosystem.models.hydrology.above_ground) calculate_temperature_effect_on_litter_decomp() (in module virtual_ecosystem.models.litter.litter_pools) calculate_temperature_effect_on_microbes() (in module virtual_ecosystem.models.soil.env_factors) calculate_theta_opt_i() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_total_C_mineralised() (in module virtual_ecosystem.models.litter.litter_pools) calculate_total_handling_time_for_herbivory() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_total_handling_time_for_predation() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) calculate_updated_pools() (in module virtual_ecosystem.models.litter.litter_pools) calculate_vapour_pressure_deficit() (in module virtual_ecosystem.models.abiotic_simple.microclimate) 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_above_canopy() (in module virtual_ecosystem.models.abiotic.wind) calculate_wind_attenuation_coefficient() (in module virtual_ecosystem.models.abiotic.wind) calculate_wind_canopy() (in module virtual_ecosystem.models.abiotic.wind) calculate_wind_profile() (in module virtual_ecosystem.models.abiotic.wind)

calculate_zero_plane_displacement() (in module virtual_ecosystem.models.abiotic.wind) 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) canopy_area (virtual_ecosystem.models.plants.community.PlantCohort attribute) canopy_layers (virtual_ecosystem.core.core_components.LayerStructure attribute) canopy_temperature_ini_factor (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) carcass_pool (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity attribute) CarcassPool (class in virtual_ecosystem.models.animals.decay) cell_area (virtual_ecosystem.core.grid.Grid attribute) cell_id (virtual_ecosystem.core.grid.Grid attribute) cell_nx (virtual_ecosystem.core.grid.Grid attribute) cell_ny (virtual_ecosystem.core.grid.Grid attribute) centroids (virtual_ecosystem.core.grid.Grid attribute) cfg_paths (virtual_ecosystem.core.config.Config attribute) cfg_strings (virtual_ecosystem.core.config.Config attribute) characteristic_dimension_leaf (virtual_ecosystem.core.constants.CoreConsts attribute) check_init_data() (virtual_ecosystem.core.base_model.BaseModel method) check_outfile() (in module virtual_ecosystem.core.utils) clay_decay (virtual_ecosystem.models.soil.env_factors.EnvironmentalEffectFactors attribute) clay_necromass_decay_exponent (virtual_ecosystem.models.soil.constants.SoilConsts attribute) 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.animals.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) collect_config_paths() (virtual_ecosystem.core.config.Config method) collect_prey() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) communities (virtual_ecosystem.models.animals.animal_model.AnimalModel attribute) (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) community_key (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity attribute) Config (class in virtual_ecosystem.core.config) config (virtual_ecosystem.core.core_components.CoreComponents attribute) (virtual_ecosystem.core.core_components.LayerStructure attribute) (virtual_ecosystem.core.core_components.ModelTiming attribute) config_errors (virtual_ecosystem.core.config.Config attribute) config_merge() (in module virtual_ecosystem.core.config) ConfigurationError constants (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity attribute) (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) (virtual_ecosystem.models.animals.plant_resources.PlantResources attribute) constants_classes (virtual_ecosystem.core.registry.ModuleInfo attribute) ConstantsDataclass (class in virtual_ecosystem.core.constants_class) construct_full_soil_model() (in module virtual_ecosystem.models.soil.soil_model) Consumer (class in virtual_ecosystem.models.animals.protocols) conversion_efficiency (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) convert_mm_flow_to_m3_per_second() (in module virtual_ecosystem.models.hydrology.above_ground) convert_soil_moisture_to_water_potential() (in module virtual_ecosystem.models.hydrology.below_ground) 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) 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.animals.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) CoreComponents (class in virtual_ecosystem.core.core_components) CoreConsts (class in virtual_ecosystem.core.constants) cue_metabolic (virtual_ecosystem.models.litter.constants.LitterConsts attribute) cue_reference_temp (virtual_ecosystem.models.soil.constants.SoilConsts attribute) cue_structural_above_ground (virtual_ecosystem.models.litter.constants.LitterConsts attribute) cue_structural_below_ground (virtual_ecosystem.models.litter.constants.LitterConsts attribute) cue_with_temperature (virtual_ecosystem.models.soil.constants.SoilConsts attribute) cue_woody (virtual_ecosystem.models.litter.constants.LitterConsts attribute)

D

damuth_density (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) damuths_law() (in module virtual_ecosystem.models.animals.scaling_functions) damuths_law_terms (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) Data (class in virtual_ecosystem.core.data) data (virtual_ecosystem.core.base_model.BaseModel attribute) (virtual_ecosystem.core.data.Data attribute) (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity attribute) (virtual_ecosystem.models.animals.animal_model.AnimalModel attribute) (virtual_ecosystem.models.animals.plant_resources.PlantResources 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) DataGenerator (class in virtual_ecosystem.core.data) dbh (virtual_ecosystem.models.plants.community.PlantCohort attribute) DECAY_FRACTION_CARCASSES (in module virtual_ecosystem.models.animals.constants) decay_fraction_carcasses (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) DECAY_FRACTION_EXCREMENT (in module virtual_ecosystem.models.animals.constants) decay_fraction_excrement (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) DecayPool (class in virtual_ecosystem.models.animals.protocols) decomposed_carbon() (virtual_ecosystem.models.animals.decay.CarcassPool method) (virtual_ecosystem.models.animals.decay.ExcrementPool method)

decomposed_energy (virtual_ecosystem.models.animals.decay.CarcassPool attribute) (virtual_ecosystem.models.animals.decay.ExcrementPool attribute) delta_mass_herbivory() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) delta_mass_predation() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) depth_of_active_soil_layer (virtual_ecosystem.core.constants.CoreConsts attribute) determine_microbial_biomass_losses() (in module virtual_ecosystem.models.soil.carbon) diabatic_correction_factor_below (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) diabatic_heat_momentum_ratio (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) die_individual() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) diet (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) DietType (class in virtual_ecosystem.models.animals.animal_traits) 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) distribute_monthly_rainfall() (in module virtual_ecosystem.models.hydrology.above_ground) docstring_style module drag_coefficient (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) drainage_map (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) dump() (virtual_ecosystem.core.grid.Grid method) dumps() (virtual_ecosystem.core.grid.Grid method)

E

eat() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) end_time (virtual_ecosystem.core.core_components.ModelTiming attribute) energetic_reserve_scaling() (in module virtual_ecosystem.models.animals.scaling_functions) energy_density (virtual_ecosystem.models.animals.plant_resources.PlantResources attribute) energy_max (virtual_ecosystem.models.animals.plant_resources.PlantResources attribute) EnvironmentalEffectFactors (class in virtual_ecosystem.models.soil.env_factors)

estimate_gpp() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) excrement_pool (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity attribute) ExcrementPool (class in virtual_ecosystem.models.animals.decay) excrete() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) export_config() (virtual_ecosystem.core.config.Config method) extinction_coefficient_global_radiation (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute)

F

F_i_j_individual() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) F_i_k() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) fat_mass_scaling() (in module virtual_ecosystem.models.animals.scaling_functions) fat_mass_terms (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) FILE_FORMAT_REGISTRY (in module virtual_ecosystem.core.readers) find_last_valid_row() (in module virtual_ecosystem.models.abiotic.abiotic_tools) find_lowest_neighbour() (in module virtual_ecosystem.models.hydrology.above_ground) find_upstream_cells() (in module virtual_ecosystem.models.hydrology.above_ground) Flora (class in virtual_ecosystem.models.plants.functional_types) flora (virtual_ecosystem.models.plants.plants_model.PlantsModel attribute) forage_cohort() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) forage_community() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) forced_conductance_parameter (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) from_cfg_strings (virtual_ecosystem.core.config.Config attribute)

from_config() (virtual_ecosystem.core.base_model.BaseModel class method) (virtual_ecosystem.core.constants_class.ConstantsDataclass 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.animals.animal_model.AnimalModel class method) (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel class method) (virtual_ecosystem.models.litter.litter_model.LitterModel class method) (virtual_ecosystem.models.plants.functional_types.Flora class method) (virtual_ecosystem.models.plants.plants_model.PlantsModel class method) (virtual_ecosystem.models.soil.soil_model.SoilModel class method) functional_group (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) functional_groups (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity attribute) (virtual_ecosystem.models.animals.animal_model.AnimalModel attribute) FunctionalGroup (class in virtual_ecosystem.models.animals.functional_group)

G

gas_constant_water_vapour (virtual_ecosystem.core.constants.CoreConsts attribute) (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) generate_canopy_model() (in module virtual_ecosystem.models.plants.canopy) generate_relative_turbulence_intensity() (in module virtual_ecosystem.models.abiotic.wind) get_community_by_key() (virtual_ecosystem.models.animals.animal_model.AnimalModel method) get_destination (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity attribute) get_distances() (virtual_ecosystem.core.grid.Grid method) get_eaten() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) (virtual_ecosystem.models.animals.plant_resources.PlantResources method) (virtual_ecosystem.models.animals.protocols.Resource method)

gpp (virtual_ecosystem.models.plants.community.PlantCohort attribute) grashof_parameter (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) gravity (virtual_ecosystem.core.constants.CoreConsts attribute) Grid (class in virtual_ecosystem.core.grid) grid (virtual_ecosystem.core.data.Data attribute) GRID_REGISTRY (in module virtual_ecosystem.core.grid) GRID_STRUCTURE_SIG (in module virtual_ecosystem.core.grid) grid_type (virtual_ecosystem.core.grid.Grid attribute) groundwater_capacity (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) groundwater_loss (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute)

H

h_herb_0 (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) H_i_j() (in module virtual_ecosystem.models.animals.scaling_functions) H_i_k() (in module virtual_ecosystem.models.animals.scaling_functions) h_pred_0 (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) half_sat_labile_C_uptake (virtual_ecosystem.models.soil.constants.SoilConsts attribute) half_sat_maom_decomposition (virtual_ecosystem.models.soil.constants.SoilConsts attribute)

half_sat_pom_decomposition (virtual_ecosystem.models.soil.constants.SoilConsts attribute) highest_optimal_pH_microbes (virtual_ecosystem.models.soil.constants.SoilConsts attribute) hydraulic_conductivity (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) hydraulic_gradient (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) HydroConsts (class in virtual_ecosystem.models.hydrology.constants) HydrologyModel (class in virtual_ecosystem.models.hydrology.hydrology_model)

I

import_functional_groups() (in module virtual_ecosystem.models.animals.functional_group) increase_age() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) increase_age_community() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) individuals (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) infiltration_shape_parameter (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) inflict_natural_mortality() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) inflict_natural_mortality_community() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) initial_air_conductivity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) initial_groundwater_saturation (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) initial_soil_moisture (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) InitialisationError initialise_absorbed_radiation() (in module virtual_ecosystem.models.abiotic.energy_balance) initialise_canopy_and_soil_fluxes() (in module virtual_ecosystem.models.abiotic.energy_balance) initialise_canopy_layers() (in module virtual_ecosystem.models.plants.canopy) initialise_canopy_temperature() (in module virtual_ecosystem.models.abiotic.energy_balance)

initialise_conductivities() (in module virtual_ecosystem.models.abiotic.conductivities) initialise_models() (in module virtual_ecosystem.main) install_example_directory() (in module virtual_ecosystem.entry_points) intake_rate (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) intake_rate_scaling() (in module virtual_ecosystem.models.animals.scaling_functions) intake_rate_terms (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) integrate() (virtual_ecosystem.models.soil.soil_model.SoilModel method) IntegrationError intercept_parameters (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) interpolate_along_heights() (in module virtual_ecosystem.models.abiotic.conductivities) interpolate_soil_temperature() (in module virtual_ecosystem.models.abiotic_simple.microclimate) is_alive (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animals.plant_resources.PlantResources attribute) is_below_mass_threshold() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) is_core (virtual_ecosystem.core.registry.ModuleInfo attribute)

J

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

K

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

k_i_k() (in module virtual_ecosystem.models.animals.scaling_functions) kinematic_viscosity_parameters (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute)

L

latent_heat_flux_linearisation() (in module virtual_ecosystem.models.abiotic.energy_balance) latent_heat_vap_equ_factors (virtual_ecosystem.models.abiotic.constants.AbioticConsts 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.animals.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) LayerStructure (class in virtual_ecosystem.core.core_components) leaf_and_air_temperature_linearisation() (in module virtual_ecosystem.models.abiotic.energy_balance) leaf_emissivity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) leaf_heat_transfer_coefficient (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) light_extinction_coefficient (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) lignin_inhibition_factor (virtual_ecosystem.models.litter.constants.LitterConsts attribute) lignin_proportion_above_structural_input (virtual_ecosystem.models.litter.constants.LitterConsts attribute) lignin_proportion_below_structural_input (virtual_ecosystem.models.litter.constants.LitterConsts attribute) lignin_proportion_wood_input (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_decay_constant_metabolic_above (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_decay_constant_metabolic_below (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_decay_constant_structural_above (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_decay_constant_structural_below (virtual_ecosystem.models.litter.constants.LitterConsts attribute)

litter_decay_constant_woody (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_decay_water_potential_halt (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_decay_water_potential_optimum (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_decomp_offset_temp (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_decomp_reference_temp (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_decomp_temp_response (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_input_to_metabolic_above (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_input_to_metabolic_below (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_input_to_structural_above (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_input_to_structural_below (virtual_ecosystem.models.litter.constants.LitterConsts attribute) litter_input_to_woody (virtual_ecosystem.models.litter.constants.LitterConsts attribute) LitterConsts (class in virtual_ecosystem.models.litter.constants) LitterModel (class in virtual_ecosystem.models.litter.litter_model) load_config_toml() (virtual_ecosystem.core.config.Config method) load_config_toml_string() (virtual_ecosystem.core.config.Config method) load_constants() (in module virtual_ecosystem.core.constants_loader) load_data_config() (virtual_ecosystem.core.data.Data method) load_netcdf() (in module virtual_ecosystem.core.readers) load_schema() (in module virtual_ecosystem.core.schema) load_to_dataarray() (in module virtual_ecosystem.core.readers) log_interpolation() (in module virtual_ecosystem.models.abiotic_simple.microclimate) LOGGER (in module virtual_ecosystem.core.logger) longevity_scaling (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) longwave_radiation_flux_linearisation() (in module virtual_ecosystem.models.abiotic.energy_balance) lowest_optimal_pH_microbes (virtual_ecosystem.models.soil.constants.SoilConsts attribute)

M

M_disp_ref (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) M_herb_0 (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) M_herb_ref (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) M_pred_ref (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) m_tol (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) m_tsm (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) maintenance_maom_enzyme (virtual_ecosystem.models.soil.constants.SoilConsts attribute) maintenance_pom_enzyme (virtual_ecosystem.models.soil.constants.SoilConsts attribute) maintenance_synthesis (virtual_ecosystem.models.soil.carbon.MicrobialBiomassLoss attribute) 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_enzyme_production (virtual_ecosystem.models.soil.carbon.MicrobialBiomassLoss attribute) maom_enzyme_turnover_rate (virtual_ecosystem.models.soil.constants.SoilConsts attribute) map_xy_to_cell_id() (virtual_ecosystem.core.grid.Grid method) map_xy_to_cell_indexing() (virtual_ecosystem.core.grid.Grid method) mass_current (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animals.plant_resources.PlantResources attribute) max_decomp_rate_maom (virtual_ecosystem.models.soil.constants.SoilConsts attribute) max_decomp_rate_pom (virtual_ecosystem.models.soil.constants.SoilConsts attribute) max_height (virtual_ecosystem.models.plants.functional_types.PlantFunctionalType attribute) max_percolation_rate_uzlz (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) max_pH_microbes (virtual_ecosystem.models.soil.constants.SoilConsts attribute) max_ratio_wind_to_friction_velocity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) max_relative_turbulence_intensity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) max_uptake_rate_labile_C (virtual_ecosystem.models.soil.constants.SoilConsts attribute) mechanical_efficiency (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) merge_conflicts (virtual_ecosystem.core.config.Config attribute) merge_continuous_data_files() (in module virtual_ecosystem.core.data) merge_schemas() (in module virtual_ecosystem.core.schema) merged_schema (virtual_ecosystem.core.config.Config attribute) metabolic_rate() (in module virtual_ecosystem.models.animals.scaling_functions) metabolic_rate_energy() (in module virtual_ecosystem.models.animals.scaling_functions) metabolic_rate_terms (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) metabolic_type (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) MetabolicType (class in virtual_ecosystem.models.animals.animal_traits) metabolize() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) metabolize_community() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) meters_to_mm (virtual_ecosystem.core.constants.CoreConsts attribute) microbial_turnover_rate (virtual_ecosystem.models.soil.constants.SoilConsts attribute) microbial_water_response_curvature (virtual_ecosystem.models.soil.constants.SoilConsts attribute) MicrobialBiomassLoss (class in virtual_ecosystem.models.soil.carbon) migrate() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) migrate_community() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) migrate_juvenile_probability() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) min_friction_velocity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) min_pH_microbes (virtual_ecosystem.models.soil.constants.SoilConsts attribute) min_relative_turbulence_intensity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) min_roughness_length (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) min_wind_speed_above_canopy (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) min_windspeed_below_canopy (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) mixing_length_factor (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) model (virtual_ecosystem.core.registry.ModuleInfo attribute) model_classes (virtual_ecosystem.core.config.Config attribute) model_constants (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) (virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel attribute) (virtual_ecosystem.models.animals.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_name (virtual_ecosystem.core.base_model.BaseModel attribute) 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.animals.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.animals.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)

ModelTiming (class in virtual_ecosystem.core.core_components) module docstring_style virtual_ecosystem.core virtual_ecosystem.core.axes virtual_ecosystem.core.base_model virtual_ecosystem.core.config virtual_ecosystem.core.constants virtual_ecosystem.core.constants_class virtual_ecosystem.core.constants_loader virtual_ecosystem.core.core_components virtual_ecosystem.core.data virtual_ecosystem.core.exceptions virtual_ecosystem.core.grid virtual_ecosystem.core.logger virtual_ecosystem.core.readers virtual_ecosystem.core.registry virtual_ecosystem.core.schema virtual_ecosystem.core.utils 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.conductivities virtual_ecosystem.models.abiotic.constants virtual_ecosystem.models.abiotic.energy_balance virtual_ecosystem.models.abiotic.soil_energy_balance virtual_ecosystem.models.abiotic.wind virtual_ecosystem.models.abiotic_simple virtual_ecosystem.models.abiotic_simple.abiotic_simple_model virtual_ecosystem.models.abiotic_simple.constants virtual_ecosystem.models.abiotic_simple.microclimate virtual_ecosystem.models.animals virtual_ecosystem.models.animals.animal_cohorts virtual_ecosystem.models.animals.animal_communities virtual_ecosystem.models.animals.animal_model virtual_ecosystem.models.animals.animal_traits virtual_ecosystem.models.animals.constants virtual_ecosystem.models.animals.decay virtual_ecosystem.models.animals.functional_group virtual_ecosystem.models.animals.plant_resources virtual_ecosystem.models.animals.protocols virtual_ecosystem.models.animals.scaling_functions virtual_ecosystem.models.hydrology virtual_ecosystem.models.hydrology.above_ground virtual_ecosystem.models.hydrology.below_ground virtual_ecosystem.models.hydrology.constants virtual_ecosystem.models.hydrology.hydrology_model virtual_ecosystem.models.litter virtual_ecosystem.models.litter.constants virtual_ecosystem.models.litter.litter_model virtual_ecosystem.models.litter.litter_pools virtual_ecosystem.models.plants virtual_ecosystem.models.plants.canopy virtual_ecosystem.models.plants.community virtual_ecosystem.models.plants.constants virtual_ecosystem.models.plants.functional_types virtual_ecosystem.models.plants.plants_model virtual_ecosystem.models.soil virtual_ecosystem.models.soil.carbon virtual_ecosystem.models.soil.constants virtual_ecosystem.models.soil.env_factors virtual_ecosystem.models.soil.soil_model MODULE_REGISTRY (in module virtual_ecosystem.core.registry) ModuleInfo (class in virtual_ecosystem.core.registry) moisture_response_curvature (virtual_ecosystem.models.litter.constants.LitterConsts attribute) molar_heat_capacity_air (virtual_ecosystem.core.constants.CoreConsts attribute) molecular_weight_air (virtual_ecosystem.core.constants.CoreConsts attribute) multiplier() (in module docstring_style) multiply_me() (docstring_style.MyClass method) muscle_mass_scaling() (in module virtual_ecosystem.models.animals.scaling_functions) muscle_mass_terms (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) myarg (docstring_style.MyClass attribute) myarg_multiple (docstring_style.MyClass attribute) MyClass (class in docstring_style)

N

n (virtual_ecosystem.models.plants.community.PlantCohort attribute) n_layers (virtual_ecosystem.core.core_components.LayerStructure attribute) N_sigma_opt_pred_prey (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) n_updates (virtual_ecosystem.core.core_components.ModelTiming attribute) name (docstring_style.MyClass attribute) (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) nan_fill_atmosphere (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute)

natural_mortality_scaling() (in module virtual_ecosystem.models.animals.scaling_functions) ncells (virtual_ecosystem.core.grid.Grid attribute) necromass_decay_to_lmwc (virtual_ecosystem.models.soil.carbon.MicrobialBiomassLoss attribute) necromass_decay_to_pom (virtual_ecosystem.models.soil.carbon.MicrobialBiomassLoss attribute) necromass_to_lmwc (virtual_ecosystem.models.soil.constants.SoilConsts attribute) negative_free_conductance_parameter (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) neighbouring_keys (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity attribute) neighbours (virtual_ecosystem.core.grid.Grid property) nonlinearily_parameter (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute)

O

o_disp (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) on_core_axis() (virtual_ecosystem.core.data.Data method)

output_current_state() (virtual_ecosystem.core.data.Data method) override_config() (virtual_ecosystem.core.config.Config method)

P

pft (virtual_ecosystem.models.plants.community.PlantCohort attribute) pft_name (virtual_ecosystem.models.plants.functional_types.PlantFunctionalType attribute) pH (virtual_ecosystem.models.soil.env_factors.EnvironmentalEffectFactors attribute) phi_herb_t (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) placeholder (virtual_ecosystem.core.constants.CoreConsts attribute) (virtual_ecosystem.models.plants.constants.PlantsConsts attribute) PlantCohort (class in virtual_ecosystem.models.plants.community) PlantCommunities (class in virtual_ecosystem.models.plants.community) PlantFunctionalType (class in virtual_ecosystem.models.plants.functional_types) PlantResources (class in virtual_ecosystem.models.animals.plant_resources) PlantsConsts (class in virtual_ecosystem.models.plants.constants)

PlantsModel (class in virtual_ecosystem.models.plants.plants_model) polygons (virtual_ecosystem.core.grid.Grid attribute) pom_decomposition_fraction_lmwc (virtual_ecosystem.models.soil.constants.SoilConsts attribute) pom_enzyme_production (virtual_ecosystem.models.soil.carbon.MicrobialBiomassLoss attribute) pom_enzyme_turnover_rate (virtual_ecosystem.models.soil.constants.SoilConsts attribute) Pool (class in virtual_ecosystem.models.animals.protocols) populate_community() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) populate_distances() (virtual_ecosystem.core.grid.Grid method) positive_free_conductance_parameter (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) prey_group_selection() (in module virtual_ecosystem.models.animals.scaling_functions) prey_groups (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) prey_scaling (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute)

R

reconciled_run_length (virtual_ecosystem.core.core_components.ModelTiming attribute) reference_cue (virtual_ecosystem.models.soil.constants.SoilConsts attribute) 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) relative_humidity (virtual_ecosystem.models.abiotic_simple.constants.AbioticSimpleBounds attribute) relative_turbulence_intensity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) remove_dead_cohort() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) remove_dead_cohort_community() (virtual_ecosystem.models.animals.animal_communities.AnimalCommunity method) remove_file_logger() (in module virtual_ecosystem.core.logger) reproductive_mass (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort attribute) required_init_vars (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.animals.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)

reservoir_const_lower_groundwater (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) reservoir_const_upper_groundwater (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) resolve_config_file_paths() (virtual_ecosystem.core.config.Config method) Resource (class in virtual_ecosystem.models.animals.protocols) richardson_bounds (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) roughness_element_drag_coefficient (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) roughness_sublayer_depth_parameter (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) run_length (virtual_ecosystem.core.core_components.ModelTiming attribute) run_length_quantity (virtual_ecosystem.core.core_components.ModelTiming attribute) run_microclimate() (in module virtual_ecosystem.models.abiotic_simple.microclimate) 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)

S

saturated_pressure_slope_parameters (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) saturation_vapour_pressure_factors (virtual_ecosystem.models.abiotic_simple.constants.AbioticSimpleConsts attribute) save_timeslice_to_netcdf() (virtual_ecosystem.core.data.Data method) save_to_netcdf() (virtual_ecosystem.core.data.Data method) scavengeable_energy (virtual_ecosystem.models.animals.decay.CarcassPool attribute) (virtual_ecosystem.models.animals.decay.ExcrementPool attribute) schema (virtual_ecosystem.core.registry.ModuleInfo attribute) seconds_to_day (virtual_ecosystem.core.constants.CoreConsts attribute) set_absorbed_irradiance() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) set_defaults() (in module virtual_ecosystem.core.schema) set_layer_roles() (in module virtual_ecosystem.core.utils) set_neighbours() (virtual_ecosystem.core.grid.Grid method) setup() (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.animals.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) sigma_f_t (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) sigma_opt_f (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) sigma_opt_pred_prey (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) simple_constants (virtual_ecosystem.models.abiotic.abiotic_model.AbioticModel attribute) soil_emissivity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) soil_layer_thickness (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) soil_layers (virtual_ecosystem.core.core_components.LayerStructure attribute) soil_microbe_water_potential_halt (virtual_ecosystem.models.soil.constants.SoilConsts attribute) soil_microbe_water_potential_optimum (virtual_ecosystem.models.soil.constants.SoilConsts attribute) soil_moisture_capacity (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) soil_moisture_residual (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) soil_protection_with_clay (virtual_ecosystem.models.soil.constants.SoilConsts attribute) soil_surface_heat_transfer_coefficient (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) soil_temperature (virtual_ecosystem.models.abiotic_simple.constants.AbioticSimpleBounds attribute)

soil_thermal_conductivity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) SoilConsts (class in virtual_ecosystem.models.soil.constants) SoilModel (class in virtual_ecosystem.models.soil.soil_model) solubility_coefficient_lmwc (virtual_ecosystem.models.soil.constants.SoilConsts 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_heat_capacity_leaf (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) specific_heat_capacity_soil (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) specific_heat_equ_factors (virtual_ecosystem.models.abiotic.constants.AbioticConsts 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.animals.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) stable_temperature_gradient_intercept (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) stable_wind_shear_slope (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) standard_mole (virtual_ecosystem.core.constants.CoreConsts attribute) standard_pressure (virtual_ecosystem.core.constants.CoreConsts attribute) start_time (virtual_ecosystem.core.core_components.ModelTiming attribute) stefan_boltzmann_constant (virtual_ecosystem.core.constants.CoreConsts attribute) stomatal_resistance (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) stored_energy (virtual_ecosystem.models.animals.plant_resources.PlantResources attribute) stream_flow_capacity (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute) subcanopy_layer_height (virtual_ecosystem.core.core_components.LayerStructure attribute) subcanopy_layer_index (virtual_ecosystem.models.hydrology.hydrology_model.HydrologyModel attribute) substrate_surface_drag_coefficient (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) surface_albedo (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) surface_layer_depth (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) surface_layer_height (virtual_ecosystem.core.core_components.LayerStructure attribute) surface_layer_index (virtual_ecosystem.models.litter.litter_model.LitterModel attribute)

T

tau_f (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) taxa (virtual_ecosystem.models.animals.functional_group.FunctionalGroup attribute) TaxaType (class in virtual_ecosystem.models.animals.animal_traits) thermal_diffusivity_parameters (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) theta_i_j() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) theta_opt_f (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) theta_opt_i() (in module virtual_ecosystem.models.animals.scaling_functions)

theta_opt_min_f (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) toml_contents (virtual_ecosystem.core.config.Config attribute) toml_files (virtual_ecosystem.core.config.Config attribute) top_leaf_air_conductivity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) top_leaf_vapour_conductivity (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) top_soil_layer_index (virtual_ecosystem.models.litter.litter_model.LitterModel attribute) (virtual_ecosystem.models.soil.soil_model.SoilModel attribute) turbulence_sign (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute)

U

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.animals.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)

update_canopy_layers() (virtual_ecosystem.models.plants.plants_model.PlantsModel method) update_carcass_pool() (virtual_ecosystem.models.animals.animal_cohorts.AnimalCohort method) update_groundwater_storage() (in module virtual_ecosystem.models.hydrology.below_ground) update_interval (virtual_ecosystem.core.core_components.ModelTiming attribute) update_interval_quantity (virtual_ecosystem.core.core_components.ModelTiming attribute) update_interval_timedelta (virtual_ecosystem.models.animals.animal_model.AnimalModel attribute) update_population_densities() (virtual_ecosystem.models.animals.animal_model.AnimalModel method) update_soil_moisture() (in module virtual_ecosystem.models.hydrology.below_ground) update_surface_temperature() (in module virtual_ecosystem.models.abiotic.soil_energy_balance)

V

V_disp (virtual_ecosystem.models.animals.constants.AnimalConsts attribute) validate_config() (virtual_ecosystem.core.config.Config method) validate_dataarray() (in module virtual_ecosystem.core.axes) validated (virtual_ecosystem.core.config.Config attribute) ValidatorWithDefaults (in module virtual_ecosystem.core.schema) vapour_pressure_deficit (virtual_ecosystem.models.abiotic_simple.constants.AbioticSimpleBounds attribute) vapour_pressure_linearisation() (in module virtual_ecosystem.models.abiotic.energy_balance) variable_validation (virtual_ecosystem.core.data.Data attribute) vars_updated (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.animals.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.constants.HydroConsts attribute) virtual_ecosystem.core module virtual_ecosystem.core.axes module virtual_ecosystem.core.base_model module virtual_ecosystem.core.config module virtual_ecosystem.core.constants module virtual_ecosystem.core.constants_class module virtual_ecosystem.core.constants_loader module virtual_ecosystem.core.core_components module virtual_ecosystem.core.data module virtual_ecosystem.core.exceptions module virtual_ecosystem.core.grid module virtual_ecosystem.core.logger module virtual_ecosystem.core.readers module virtual_ecosystem.core.registry module virtual_ecosystem.core.schema module virtual_ecosystem.core.utils 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.conductivities module virtual_ecosystem.models.abiotic.constants module virtual_ecosystem.models.abiotic.energy_balance module virtual_ecosystem.models.abiotic.soil_energy_balance 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.constants module virtual_ecosystem.models.abiotic_simple.microclimate module virtual_ecosystem.models.animals module virtual_ecosystem.models.animals.animal_cohorts module virtual_ecosystem.models.animals.animal_communities module virtual_ecosystem.models.animals.animal_model module virtual_ecosystem.models.animals.animal_traits module virtual_ecosystem.models.animals.constants module virtual_ecosystem.models.animals.decay module virtual_ecosystem.models.animals.functional_group module virtual_ecosystem.models.animals.plant_resources module virtual_ecosystem.models.animals.protocols module virtual_ecosystem.models.animals.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.constants module virtual_ecosystem.models.hydrology.hydrology_model module virtual_ecosystem.models.litter module virtual_ecosystem.models.litter.constants module virtual_ecosystem.models.litter.litter_model module virtual_ecosystem.models.litter.litter_pools module virtual_ecosystem.models.plants module virtual_ecosystem.models.plants.canopy module virtual_ecosystem.models.plants.community module virtual_ecosystem.models.plants.constants module virtual_ecosystem.models.plants.functional_types module virtual_ecosystem.models.plants.plants_model module virtual_ecosystem.models.soil module virtual_ecosystem.models.soil.carbon module virtual_ecosystem.models.soil.constants module virtual_ecosystem.models.soil.env_factors module virtual_ecosystem.models.soil.soil_model module volume_to_weight_conversion (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) von_karmans_constant (virtual_ecosystem.core.constants.CoreConsts attribute)

W

w_bar_i_j() (in module virtual_ecosystem.models.animals.scaling_functions) water (virtual_ecosystem.models.soil.env_factors.EnvironmentalEffectFactors attribute) water_retention_curvature (virtual_ecosystem.models.hydrology.constants.HydroConsts attribute)

wind_log_profile() (in module virtual_ecosystem.models.abiotic.wind) wind_profile_parameters (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute) wind_reference_height (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute)

X

xoff (virtual_ecosystem.core.grid.Grid attribute)

Y

yasuda_stability_parameters (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute)

yoff (virtual_ecosystem.core.grid.Grid attribute)

Z

zero_Celsius (virtual_ecosystem.core.constants.CoreConsts attribute)

zero_plane_scaling_parameter (virtual_ecosystem.models.abiotic.constants.AbioticConsts attribute)