Welcome to the Virtual Ecosystem
This repository is the home for the development of the Virtual Ecosystem. The Virtual Ecosystem is a project to develop a simulation of all of the major processes involved in a real ecosystem including the:
growth and demographic processes of the primary producers within the forest,
microclimatic processes within and around the ecosystem,
hydrological processes within the canopy, soil and drainage networks,
biotic and abiotic processes within the soil, and the
growth and demography of heterotrophs.
Project details
This project is funded by a 2021 Distinguished Scientist award from the NOMIS Foundation to Professor Robert Ewers:
The research is based at Imperial College London:
Project Team
Professor Robert Ewers
Olivia Daniel
Dr. Jaideep Joshi
Dr. David Orme
Dr. Vivienne Groner
Dr. Jacob Cook
Dr. Taran Rallings
The research team are supported by the Imperial College London Research Software Engineering team.
The Virtual Ecosystem
- The Virtual Ecosystem models
- Basic Virtual Ecosystem model usage
- Virtual Ecosystem example data
- Virtual Ecosystem simulation flow
- Virtual Ecosystem parameterisation
- Further details of soil module
- The
core.gridmodule - Adding and using data with the Virtual Ecosystem
- Core axes
- The configuration module
API reference
- Main
- Example data
- Core Overview
- Configuration
ConfigConfig.build_config()Config.build_schema()Config.cfg_pathsConfig.cfg_stringsConfig.collect_config_paths()Config.config_errorsConfig.export_config()Config.from_cfg_stringsConfig.load_config_toml()Config.load_config_toml_string()Config.merge_conflictsConfig.merged_schemaConfig.model_classesConfig.override_config()Config.resolve_config_file_paths()Config.toml_contentsConfig.toml_filesConfig.validate_config()Config.validated
config_merge()
- Logger
- Grid
GRID_REGISTRYGRID_STRUCTURE_SIGGridGrid.__repr__()Grid.boundsGrid.cell_areaGrid.cell_idGrid.cell_nxGrid.cell_nyGrid.centroidsGrid.dump()Grid.dumps()Grid.from_config()Grid.get_distances()Grid.grid_typeGrid.map_xy_to_cell_id()Grid.map_xy_to_cell_indexing()Grid.ncellsGrid.neighboursGrid.polygonsGrid.populate_distances()Grid.set_neighbours()Grid.xoffGrid.yoff
make_hex_grid()make_square_grid()register_grid()
- Data
- File readers
- Core axes
- Base Model
- Declaring new subclasses
- Model checking
- The
BaseModel.__init__method - The
from_configfactory method - Model registration
BaseModelBaseModel.__init__()BaseModel.__init_subclass__()BaseModel.__repr__()BaseModel.__str__()BaseModel._check_model_name()BaseModel._check_model_update_bounds()BaseModel._check_required_init_vars()BaseModel._check_vars_updated()BaseModel.check_init_data()BaseModel.cleanup()BaseModel.core_constantsBaseModel.dataBaseModel.from_config()BaseModel.layer_structureBaseModel.model_nameBaseModel.model_timingBaseModel.model_update_boundsBaseModel.required_init_varsBaseModel.setup()BaseModel.spinup()BaseModel.update()BaseModel.vars_updated
- Core Components
- Core Constants
CoreConstsCoreConsts.characteristic_dimension_leafCoreConsts.depth_of_active_soil_layerCoreConsts.gas_constant_water_vapourCoreConsts.gravityCoreConsts.meters_to_mmCoreConsts.molar_heat_capacity_airCoreConsts.molecular_weight_airCoreConsts.placeholderCoreConsts.seconds_to_dayCoreConsts.standard_moleCoreConsts.standard_pressureCoreConsts.stefan_boltzmann_constantCoreConsts.von_karmans_constantCoreConsts.zero_Celsius
- Constants Classes
- Constants Loader
- Schema
- Module Registry
- Utility functions
- Custom exceptions
- Soil Overview
- Soil Model
IntegrationErrorSoilModelSoilModel.cleanup()SoilModel.core_constantsSoilModel.dataSoilModel.from_config()SoilModel.integrate()SoilModel.layer_structureSoilModel.model_constantsSoilModel.model_timingSoilModel.model_update_boundsSoilModel.required_init_varsSoilModel.setup()SoilModel.spinup()SoilModel.top_soil_layer_indexSoilModel.update()SoilModel.vars_updated
construct_full_soil_model()make_slices()
- Soil Carbon
- Soil Environmental Factors
- Soil Constants
SoilConstsSoilConsts.activation_energy_labile_C_saturationSoilConsts.activation_energy_maom_decomp_rateSoilConsts.activation_energy_maom_decomp_saturationSoilConsts.activation_energy_microbial_turnoverSoilConsts.activation_energy_microbial_uptakeSoilConsts.activation_energy_pom_decomp_rateSoilConsts.activation_energy_pom_decomp_saturationSoilConsts.arrhenius_reference_tempSoilConsts.base_soil_protectionSoilConsts.clay_necromass_decay_exponentSoilConsts.cue_reference_tempSoilConsts.cue_with_temperatureSoilConsts.half_sat_labile_C_uptakeSoilConsts.half_sat_maom_decompositionSoilConsts.half_sat_pom_decompositionSoilConsts.highest_optimal_pH_microbesSoilConsts.lowest_optimal_pH_microbesSoilConsts.maintenance_maom_enzymeSoilConsts.maintenance_pom_enzymeSoilConsts.maom_enzyme_turnover_rateSoilConsts.max_decomp_rate_maomSoilConsts.max_decomp_rate_pomSoilConsts.max_pH_microbesSoilConsts.max_uptake_rate_labile_CSoilConsts.microbial_turnover_rateSoilConsts.microbial_water_response_curvatureSoilConsts.min_pH_microbesSoilConsts.necromass_to_lmwcSoilConsts.pom_decomposition_fraction_lmwcSoilConsts.pom_enzyme_turnover_rateSoilConsts.reference_cueSoilConsts.soil_microbe_water_potential_haltSoilConsts.soil_microbe_water_potential_optimumSoilConsts.soil_protection_with_claySoilConsts.solubility_coefficient_lmwc
- Abiotic Simple Overview
- Abiotic Simple Model
- The
AbioticSimpleModelclassAbioticSimpleModelAbioticSimpleModel.boundsAbioticSimpleModel.cleanup()AbioticSimpleModel.core_constantsAbioticSimpleModel.dataAbioticSimpleModel.from_config()AbioticSimpleModel.layer_structureAbioticSimpleModel.model_constantsAbioticSimpleModel.model_timingAbioticSimpleModel.model_update_boundsAbioticSimpleModel.required_init_varsAbioticSimpleModel.setup()AbioticSimpleModel.spinup()AbioticSimpleModel.update()AbioticSimpleModel.vars_updated
- The
- Abiotic Simple Microclimate
- Abiotic Simple Constants
- Abiotic Mechanistic Overview
- Abiotic Mechanistic Model
- The
AbioticModelclassAbioticModelAbioticModel.cleanup()AbioticModel.core_constantsAbioticModel.dataAbioticModel.from_config()AbioticModel.layer_structureAbioticModel.model_constantsAbioticModel.model_timingAbioticModel.model_update_boundsAbioticModel.required_init_varsAbioticModel.setup()AbioticModel.spinup()AbioticModel.update()AbioticModel.vars_updated
- The
- Abiotic Mechanistic Constants
AbioticConstsAbioticConsts.__init__()AbioticConsts.bottom_leaf_air_conductivityAbioticConsts.bottom_leaf_vapour_conductivityAbioticConsts.canopy_temperature_ini_factorAbioticConsts.diabatic_correction_factor_belowAbioticConsts.diabatic_heat_momentum_ratioAbioticConsts.drag_coefficientAbioticConsts.forced_conductance_parameterAbioticConsts.gas_constant_water_vapourAbioticConsts.grashof_parameterAbioticConsts.initial_air_conductivityAbioticConsts.kinematic_viscosity_parametersAbioticConsts.latent_heat_vap_equ_factorsAbioticConsts.leaf_emissivityAbioticConsts.leaf_heat_transfer_coefficientAbioticConsts.light_extinction_coefficientAbioticConsts.max_ratio_wind_to_friction_velocityAbioticConsts.max_relative_turbulence_intensityAbioticConsts.min_relative_turbulence_intensityAbioticConsts.min_roughness_lengthAbioticConsts.min_wind_speed_above_canopyAbioticConsts.min_windspeed_below_canopyAbioticConsts.mixing_length_factorAbioticConsts.negative_free_conductance_parameterAbioticConsts.positive_free_conductance_parameterAbioticConsts.relative_turbulence_intensityAbioticConsts.roughness_element_drag_coefficientAbioticConsts.roughness_sublayer_depth_parameterAbioticConsts.soil_emissivityAbioticConsts.soil_thermal_conductivityAbioticConsts.specific_heat_capacity_leafAbioticConsts.specific_heat_capacity_soilAbioticConsts.specific_heat_equ_factorsAbioticConsts.stomatal_resistanceAbioticConsts.substrate_surface_drag_coefficientAbioticConsts.surface_albedoAbioticConsts.surface_layer_depthAbioticConsts.thermal_diffusivity_parametersAbioticConsts.top_leaf_air_conductivityAbioticConsts.top_leaf_vapour_conductivityAbioticConsts.turbulence_signAbioticConsts.volume_to_weight_conversionAbioticConsts.yasuda_stability_parametersAbioticConsts.zero_plane_scaling_parameter
- Abiotic Mechanistic Tools
- Abiotic Mechanistic Wind
calculate_diabatic_correction_above()calculate_friction_velocity()calculate_mean_mixing_length()calculate_roughness_length_momentum()calculate_wind_above_canopy()calculate_wind_attenuation_coefficient()calculate_wind_canopy()calculate_wind_profile()calculate_zero_plane_displacement()generate_relative_turbulence_intensity()wind_log_profile()
- Abiotic Mechanistic Energy Balance
calculate_delta_canopy_temperature()calculate_leaf_and_air_temperature()calculate_longwave_emission()calculate_slope_of_saturated_pressure_curve()initialise_absorbed_radiation()initialise_canopy_and_soil_fluxes()initialise_canopy_temperature()latent_heat_flux_linearisation()leaf_and_air_temperature_linearisation()longwave_radiation_flux_linearisation()vapour_pressure_linearisation()
- Abiotic Mechanistic Soil Energy Balance
- Abiotic Mechanistic Conductivities
- Hydrology Overview
- Hydrology Model
HydrologyModelHydrologyModel.cleanup()HydrologyModel.core_constantsHydrologyModel.dataHydrologyModel.drainage_mapHydrologyModel.from_config()HydrologyModel.initial_groundwater_saturationHydrologyModel.initial_soil_moistureHydrologyModel.layer_structureHydrologyModel.model_constantsHydrologyModel.model_timingHydrologyModel.model_update_boundsHydrologyModel.required_init_varsHydrologyModel.setup()HydrologyModel.spinup()HydrologyModel.update()HydrologyModel.vars_updated
calculate_layer_thickness()setup_hydrology_input_current_timestep()
- Hydrology Above-ground
- Hydrology Below-ground
- Hydrology Constants
HydroConstsHydroConsts.__init__()HydroConsts.air_entry_water_potentialHydroConsts.extinction_coefficient_global_radiationHydroConsts.groundwater_capacityHydroConsts.groundwater_lossHydroConsts.hydraulic_conductivityHydroConsts.hydraulic_gradientHydroConsts.infiltration_shape_parameterHydroConsts.intercept_parametersHydroConsts.max_percolation_rate_uzlzHydroConsts.nonlinearily_parameterHydroConsts.reservoir_const_lower_groundwaterHydroConsts.reservoir_const_upper_groundwaterHydroConsts.soil_moisture_capacityHydroConsts.soil_moisture_residualHydroConsts.soil_surface_heat_transfer_coefficientHydroConsts.stream_flow_capacityHydroConsts.veg_density_paramHydroConsts.water_retention_curvature
- Animal Overview
- Animal Model
AnimalModelAnimalModel.calculate_density_for_cohort()AnimalModel.calculate_litter_additions()AnimalModel.cleanup()AnimalModel.communitiesAnimalModel.core_constantsAnimalModel.dataAnimalModel.from_config()AnimalModel.functional_groupsAnimalModel.get_community_by_key()AnimalModel.layer_structureAnimalModel.model_constantsAnimalModel.model_timingAnimalModel.model_update_boundsAnimalModel.required_init_varsAnimalModel.setup()AnimalModel.spinup()AnimalModel.update()AnimalModel.update_interval_timedeltaAnimalModel.update_population_densities()AnimalModel.vars_updated
- Animal Communities
AnimalCommunityAnimalCommunity.all_animal_cohortsAnimalCommunity.animal_cohortsAnimalCommunity.birth()AnimalCommunity.birth_community()AnimalCommunity.carcass_poolAnimalCommunity.collect_prey()AnimalCommunity.community_keyAnimalCommunity.constantsAnimalCommunity.dataAnimalCommunity.excrement_poolAnimalCommunity.forage_community()AnimalCommunity.functional_groupsAnimalCommunity.get_destinationAnimalCommunity.increase_age_community()AnimalCommunity.inflict_natural_mortality_community()AnimalCommunity.metabolize_community()AnimalCommunity.migrate()AnimalCommunity.migrate_community()AnimalCommunity.neighbouring_keysAnimalCommunity.populate_community()AnimalCommunity.remove_dead_cohort()AnimalCommunity.remove_dead_cohort_community()
- Animal Protocols
- Animal Cohorts
AnimalCohortAnimalCohort.F_i_j_individual()AnimalCohort.F_i_k()AnimalCohort.adult_natural_mortality_probAnimalCohort.ageAnimalCohort.calculate_alpha()AnimalCohort.calculate_consumed_mass_herbivory()AnimalCohort.calculate_consumed_mass_predation()AnimalCohort.calculate_potential_consumed_biomass()AnimalCohort.calculate_potential_prey_consumed()AnimalCohort.calculate_predation_search_rate()AnimalCohort.calculate_predation_success_probability()AnimalCohort.calculate_theta_opt_i()AnimalCohort.calculate_total_handling_time_for_herbivory()AnimalCohort.calculate_total_handling_time_for_predation()AnimalCohort.constantsAnimalCohort.damuth_densityAnimalCohort.decay_fraction_carcassesAnimalCohort.decay_fraction_excrementAnimalCohort.delta_mass_herbivory()AnimalCohort.delta_mass_predation()AnimalCohort.die_individual()AnimalCohort.eat()AnimalCohort.excrete()AnimalCohort.forage_cohort()AnimalCohort.functional_groupAnimalCohort.get_eaten()AnimalCohort.increase_age()AnimalCohort.individualsAnimalCohort.inflict_natural_mortality()AnimalCohort.intake_rateAnimalCohort.is_aliveAnimalCohort.is_below_mass_threshold()AnimalCohort.mass_currentAnimalCohort.metabolize()AnimalCohort.nameAnimalCohort.prey_groupsAnimalCohort.reproductive_massAnimalCohort.theta_i_j()AnimalCohort.update_carcass_pool()
- Animal Functional Groups
FunctionalGroupFunctionalGroup.adult_massFunctionalGroup.birth_massFunctionalGroup.constantsFunctionalGroup.conversion_efficiencyFunctionalGroup.damuths_law_termsFunctionalGroup.dietFunctionalGroup.fat_mass_termsFunctionalGroup.intake_rate_termsFunctionalGroup.longevity_scalingFunctionalGroup.mechanical_efficiencyFunctionalGroup.metabolic_rate_termsFunctionalGroup.metabolic_typeFunctionalGroup.muscle_mass_termsFunctionalGroup.nameFunctionalGroup.prey_scalingFunctionalGroup.taxa
import_functional_groups()
- Animal Traits
- Animal Scaling Functions
- Animal Constants
AnimalConstsAnimalConsts.M_herb_0AnimalConsts.M_herb_refAnimalConsts.M_pred_refAnimalConsts.N_sigma_opt_pred_preyAnimalConsts.alpha_0_herbAnimalConsts.alpha_0_predAnimalConsts.b_herbAnimalConsts.b_predAnimalConsts.c_tolAnimalConsts.c_tsmAnimalConsts.h_herb_0AnimalConsts.h_pred_0AnimalConsts.m_tolAnimalConsts.m_tsmAnimalConsts.phi_herb_tAnimalConsts.sigma_f_tAnimalConsts.sigma_opt_fAnimalConsts.sigma_opt_pred_preyAnimalConsts.tau_fAnimalConsts.theta_opt_fAnimalConsts.theta_opt_min_f
DECAY_FRACTION_CARCASSESDECAY_FRACTION_EXCREMENT
- Animal Decay
- Animal Plant Resources
- Litter Overview
- Litter Model
LitterModelLitterModel.cleanup()LitterModel.core_constantsLitterModel.dataLitterModel.from_config()LitterModel.layer_structureLitterModel.model_constantsLitterModel.model_timingLitterModel.model_update_boundsLitterModel.required_init_varsLitterModel.setup()LitterModel.spinup()LitterModel.surface_layer_indexLitterModel.top_soil_layer_indexLitterModel.update()LitterModel.vars_updated
- Litter Pools
calculate_carbon_mineralised()calculate_change_in_lignin()calculate_change_in_litter_variables()calculate_decay_rates()calculate_environmental_factors()calculate_lignin_updates()calculate_litter_chemistry_factor()calculate_litter_decay_metabolic_above()calculate_litter_decay_metabolic_below()calculate_litter_decay_structural_above()calculate_litter_decay_structural_below()calculate_litter_decay_woody()calculate_moisture_effect_on_litter_decomp()calculate_temperature_effect_on_litter_decomp()calculate_total_C_mineralised()calculate_updated_pools()
- Litter Constants
LitterConstsLitterConsts.cue_metabolicLitterConsts.cue_structural_above_groundLitterConsts.cue_structural_below_groundLitterConsts.cue_woodyLitterConsts.lignin_inhibition_factorLitterConsts.lignin_proportion_above_structural_inputLitterConsts.lignin_proportion_below_structural_inputLitterConsts.lignin_proportion_wood_inputLitterConsts.litter_decay_constant_metabolic_aboveLitterConsts.litter_decay_constant_metabolic_belowLitterConsts.litter_decay_constant_structural_aboveLitterConsts.litter_decay_constant_structural_belowLitterConsts.litter_decay_constant_woodyLitterConsts.litter_decay_water_potential_haltLitterConsts.litter_decay_water_potential_optimumLitterConsts.litter_decomp_offset_tempLitterConsts.litter_decomp_reference_tempLitterConsts.litter_decomp_temp_responseLitterConsts.litter_input_to_metabolic_aboveLitterConsts.litter_input_to_metabolic_belowLitterConsts.litter_input_to_structural_aboveLitterConsts.litter_input_to_structural_belowLitterConsts.litter_input_to_woodyLitterConsts.moisture_response_curvature
- Plants Model
- The
plants_modelmodulePlantsModelPlantsModel.allocate_gpp()PlantsModel.cleanup()PlantsModel.communitiesPlantsModel.core_constantsPlantsModel.dataPlantsModel.estimate_gpp()PlantsModel.floraPlantsModel.from_config()PlantsModel.layer_structurePlantsModel.model_constantsPlantsModel.model_timingPlantsModel.model_update_boundsPlantsModel.required_init_varsPlantsModel.set_absorbed_irradiance()PlantsModel.setup()PlantsModel.spinup()PlantsModel.update()PlantsModel.update_canopy_layers()PlantsModel.vars_updated
- The plants
constantsmodule
- The
- Plants Structures
Command line tools
Development
- Strategy
- Developer Setup
- Documentation Overview
- Jupyter Notebooks
- Docstring Style
- API Generation
- Core Design
- Adding New Models
- Package Releases
Climate data resources
Bibliography