Index

A

acidity (seapopym.configuration.acidity.forcing_parameter.ForcingParameter attribute) (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) (seapopym.standard.units.StandardUnitsLabels attribute) AcidityBedModel (class in seapopym.model.acidity_model) AcidityConfiguration (class in seapopym.configuration.acidity.configuration) AcidityModel (class in seapopym.model.acidity_model) age_to_dataset() (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit method) ageing() (in module seapopym.function.compiled_functions.production_compiled_functions) all_forcings (seapopym.configuration.no_transport.forcing_parameter.ForcingParameter property) angle_horizon_sun (seapopym.configuration.no_transport.kernel_parameter.KernelParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute)

apply_coefficient_to_primary_production_desc (in module seapopym.standard.attributs) apply_mask_to_state() (in module seapopym.function.apply_mask_to_state) are_all_instance_of_functional_group_unit() (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupParameter method) as_dict() (seapopym.configuration.no_transport.forcing_parameter.ChunkParameter method) (seapopym.standard.ChunkParameterProtocol method) attrs (seapopym.core.template.TemplateUnit attribute) average_acidity() (in module seapopym.function.average_acidity) average_temperature() (in module seapopym.function.average_temperature) avg_acidity_by_fgroup (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) avg_temperature_by_fgroup (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute)

B

BaseTemplate (class in seapopym.core.template) biomass (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) (seapopym.standard.units.StandardUnitsLabels attribute)

biomass() (in module seapopym.function.biomass) biomass_sequence() (in module seapopym.function.compiled_functions.biomass_compiled_functions)

C

cell_area (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) cell_area() (in module seapopym.function.cell_area) check_cohort_timestep() (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit method) chunk (seapopym.configuration.no_transport.forcing_parameter.ForcingParameter attribute) (seapopym.standard.ForcingParameterProtocol attribute) ChunkParameter (class in seapopym.configuration.no_transport.forcing_parameter) ChunkParameterProtocol (class in seapopym.standard) chunks (seapopym.core.template.TemplateUnit attribute) cohort (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.CoordinatesLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) (seapopym.standard.labels.CoordinatesLabels attribute) cohort_timestep (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit attribute)

compute_cell_area_desc (in module seapopym.standard.attributs) compute_initial_conditions (seapopym.configuration.no_transport.kernel_parameter.KernelParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) compute_limits_from_zeu_lat_sst() (in module seapopym.function.limits) compute_preproduction (seapopym.configuration.no_transport.kernel_parameter.KernelParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) ConfigurationLabels (class in seapopym.standard) (class in seapopym.standard.labels) ConfigurationProtocol (class in seapopym.standard) convert() (seapopym.configuration.no_transport.forcing_parameter.ForcingUnit method) CoordinateAuthority (class in seapopym.standard) CoordinatesLabels (class in seapopym.standard) (class in seapopym.standard.labels)

D

day_layer (seapopym.configuration.no_transport.functional_group_parameter.MigratoryTypeParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) day_length (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute)

day_length() (in module seapopym.function.day_length) depth (seapopym.standard.labels.SeaLayers property) dims (seapopym.core.template.TemplateUnit attribute) dtype (seapopym.core.template.TemplateUnit attribute)

E

energy_transfert (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) ensure_coordinate_integrity() (seapopym.standard.CoordinateAuthority method)

EPI (seapopym.standard.labels.SeaLayers attribute) expand_dims() (in module seapopym.function.compiled_functions.production_compiled_functions) expected_memory_usage (seapopym.model.no_transport_model.NoTransportModel property) export_initial_conditions() (seapopym.model.no_transport_model.NoTransportModel method)

F

fgroup_name (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) forcing (seapopym.configuration.acidity.configuration.AcidityConfiguration attribute) (seapopym.configuration.no_transport.configuration.NoTransportConfiguration attribute) (seapopym.configuration.no_transport.forcing_parameter.ForcingUnit attribute) (seapopym.standard.ConfigurationProtocol attribute) ForcingLabels (class in seapopym.standard) (class in seapopym.standard.labels) ForcingParameter (class in seapopym.configuration.acidity.forcing_parameter) (class in seapopym.configuration.no_transport.forcing_parameter) ForcingParameterProtocol (class in seapopym.standard) ForcingUnit (class in seapopym.configuration.no_transport.forcing_parameter) format_unit_string() (seapopym.standard.StandardUnitsRegistry static method) (seapopym.standard.units.StandardUnitsRegistry static method) from_configuration() (seapopym.model.acidity_model.AcidityBedModel class method) (seapopym.model.acidity_model.AcidityModel class method) (seapopym.model.no_transport_model.NoTransportLightModel class method) (seapopym.model.no_transport_model.NoTransportModel class method) (seapopym.model.no_transport_model.NoTransportSpaceOptimizedLightModel class method) (seapopym.standard.ModelProtocol class method) from_dataset() (seapopym.configuration.no_transport.forcing_parameter.ForcingUnit class method)

from_path() (seapopym.configuration.no_transport.forcing_parameter.ForcingUnit class method) function (seapopym.core.kernel.KernelUnit attribute) functional_group (seapopym.configuration.acidity.configuration.AcidityConfiguration attribute) (seapopym.configuration.acidity.functional_group_parameter.FunctionalGroupParameter attribute) (seapopym.configuration.no_transport.configuration.NoTransportConfiguration attribute) (seapopym.configuration.no_transport.forcing_parameter.ChunkParameter attribute) (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupParameter attribute) (seapopym.standard.ConfigurationProtocol attribute) (seapopym.standard.CoordinatesLabels attribute) (seapopym.standard.FunctionalGroupParameterProtocol attribute) (seapopym.standard.labels.CoordinatesLabels attribute) functional_group_desc() (in module seapopym.standard.attributs) functional_type (seapopym.configuration.acidity.functional_group_parameter.FunctionalGroupUnit attribute) (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit attribute) FunctionalGroupParameter (class in seapopym.configuration.acidity.functional_group_parameter) (class in seapopym.configuration.no_transport.functional_group_parameter) FunctionalGroupParameterProtocol (class in seapopym.standard) FunctionalGroupUnit (class in seapopym.configuration.acidity.functional_group_parameter) (class in seapopym.configuration.no_transport.functional_group_parameter) FunctionalTypeParameter (class in seapopym.configuration.acidity.functional_group_parameter) (class in seapopym.configuration.no_transport.functional_group_parameter)

G

gamma_lambda_acidity (seapopym.configuration.acidity.functional_group_parameter.FunctionalTypeParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) gamma_lambda_temperature (seapopym.configuration.no_transport.functional_group_parameter.FunctionalTypeParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) gamma_survival_rate_acidity (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) gamma_survival_rate_temperature (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) gamma_tr (seapopym.configuration.no_transport.functional_group_parameter.FunctionalTypeParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute)

generate() (seapopym.core.template.BaseTemplate method) (seapopym.core.template.Template method) (seapopym.core.template.TemplateUnit method) (seapopym.standard.TemplateProtocol method) get_coordinate_attrs() (seapopym.standard.CoordinateAuthority method) get_registered_coordinates() (seapopym.standard.CoordinateAuthority class method) get_supported_units() (seapopym.standard.StandardUnitsRegistry static method) (seapopym.standard.units.StandardUnitsRegistry static method) get_unit_attrs() (seapopym.standard.StandardUnitsRegistry static method) (seapopym.standard.units.StandardUnitsRegistry static method) global_mask (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) global_mask() (in module seapopym.function.global_mask) global_mask_desc (in module seapopym.standard.attributs)

H

height (seapopym.standard.units.StandardUnitsLabels attribute)

I

initial_condition_biomass (seapopym.configuration.no_transport.forcing_parameter.ForcingParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) initial_condition_production (seapopym.configuration.no_transport.forcing_parameter.ForcingParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute)

initialize_defaults() (seapopym.standard.CoordinateAuthority class method) is_coordinate_valid() (seapopym.standard.CoordinateAuthority method)

K

Kernel (class in seapopym.core.kernel) kernel (seapopym.configuration.no_transport.configuration.NoTransportConfiguration attribute) (seapopym.model.no_transport_model.NoTransportModel attribute) (seapopym.standard.ConfigurationProtocol attribute) (seapopym.standard.ModelProtocol attribute)

kernel_factory() (in module seapopym.core.kernel) kernel_unit_factory() (in module seapopym.core.kernel) KernelParameter (class in seapopym.configuration.no_transport.kernel_parameter) KernelParameterProtocol (class in seapopym.standard) KernelUnit (class in seapopym.core.kernel)

L

lambda_0 (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) lambda_acidity_0 (seapopym.configuration.acidity.functional_group_parameter.FunctionalTypeParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute)

lambda_temperature_0 (seapopym.configuration.no_transport.functional_group_parameter.FunctionalTypeParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) LOWMESO (seapopym.standard.labels.SeaLayers attribute)

M

mask_by_fgroup (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) mask_by_fgroup() (in module seapopym.function.mask_by_functional_group) mask_by_fgroup_desc (in module seapopym.standard.attributs) mask_temperature (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) mask_temperature() (in module seapopym.function.mask_temperature) mask_temperature_desc (in module seapopym.standard.attributs) max_timestep (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) mean_timestep (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) migratory_type (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit attribute) MigratoryTypeParameter (class in seapopym.configuration.no_transport.functional_group_parameter) min_temperature (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) min_temperature_by_cohort() (in module seapopym.function.min_temperature) min_temperature_by_cohort_desc (in module seapopym.standard.attributs) min_timestep (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) ModelProtocol (class in seapopym.standard) module seapopym seapopym.configuration seapopym.configuration.acidity seapopym.configuration.acidity.configuration seapopym.configuration.acidity.forcing_parameter seapopym.configuration.acidity.functional_group_parameter seapopym.configuration.no_transport seapopym.configuration.no_transport.configuration seapopym.configuration.no_transport.forcing_parameter seapopym.configuration.no_transport.functional_group_parameter seapopym.configuration.no_transport.kernel_parameter seapopym.core seapopym.core.kernel seapopym.core.template seapopym.function seapopym.function.apply_coefficient_to_primary_production seapopym.function.apply_mask_to_state seapopym.function.average_acidity seapopym.function.average_temperature seapopym.function.biomass seapopym.function.cell_area seapopym.function.compiled_functions seapopym.function.compiled_functions.biomass_compiled_functions seapopym.function.compiled_functions.production_compiled_functions seapopym.function.day_length seapopym.function.global_mask seapopym.function.limits seapopym.function.mask_by_functional_group seapopym.function.mask_temperature seapopym.function.min_temperature seapopym.function.mortality_acidity_field seapopym.function.mortality_field seapopym.function.production seapopym.model seapopym.model.acidity_model seapopym.model.no_transport_model seapopym.standard seapopym.standard.attributs seapopym.standard.coordinates seapopym.standard.labels seapopym.standard.types seapopym.standard.units

mortality_acidity_bed_field() (in module seapopym.function.mortality_acidity_field) mortality_acidity_field() (in module seapopym.function.mortality_acidity_field) mortality_field (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) mortality_field() (in module seapopym.function.mortality_field) mortality_field_desc (in module seapopym.standard.attributs)

N

name (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit attribute) (seapopym.core.kernel.KernelUnit attribute) (seapopym.core.template.TemplateUnit attribute) new_cohort() (in module seapopym.standard.coordinates) new_latitude() (in module seapopym.standard.coordinates) new_layer() (in module seapopym.standard.coordinates) new_longitude() (in module seapopym.standard.coordinates)

new_time() (in module seapopym.standard.coordinates) night_layer (seapopym.configuration.no_transport.functional_group_parameter.MigratoryTypeParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) NoTransportConfiguration (class in seapopym.configuration.no_transport.configuration) NoTransportLightModel (class in seapopym.model.no_transport_model) NoTransportModel (class in seapopym.model.no_transport_model) NoTransportSpaceOptimizedLightModel (class in seapopym.model.no_transport_model)

O

order_data() (seapopym.standard.CoordinatesLabels class method) (seapopym.standard.labels.CoordinatesLabels class method)

ordered() (seapopym.standard.CoordinatesLabels class method) (seapopym.standard.labels.CoordinatesLabels class method)

P

parallel (seapopym.configuration.no_transport.forcing_parameter.ForcingParameter attribute) (seapopym.core.kernel.KernelUnit attribute) (seapopym.standard.ForcingParameterProtocol attribute) parameter_to_dataset (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit attribute) parse() (seapopym.configuration.no_transport.configuration.NoTransportConfiguration class method) (seapopym.standard.ConfigurationProtocol class method) path_validation() (in module seapopym.configuration.no_transport.forcing_parameter) preproduction (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) primary_production (seapopym.configuration.no_transport.forcing_parameter.ForcingParameter attribute) (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute)

primary_production_by_fgroup (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) primary_production_by_fgroup() (in module seapopym.function.apply_coefficient_to_primary_production) production (seapopym.standard.units.StandardUnitsLabels attribute) production() (in module seapopym.function.compiled_functions.production_compiled_functions) (in module seapopym.function.production) production_export_initial() (in module seapopym.function.compiled_functions.production_compiled_functions) production_export_preproduction() (in module seapopym.function.compiled_functions.production_compiled_functions) production_initial_condition() (in module seapopym.function.production) production_space_optimized() (in module seapopym.function.compiled_functions.production_compiled_functions) (in module seapopym.function.production) production_unrecruited() (in module seapopym.function.production)

R

recruited (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) register_coordinate() (seapopym.standard.CoordinateAuthority class method) reorder_dims() (in module seapopym.standard.coordinates) resolution_latitude (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute)

resolution_longitude (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) run() (seapopym.core.kernel.Kernel method) (seapopym.core.kernel.KernelUnit method) (seapopym.model.no_transport_model.NoTransportModel method) (seapopym.standard.ModelProtocol method)

S

SeaLayers (class in seapopym.standard.labels) seapopym module seapopym.configuration module seapopym.configuration.acidity module seapopym.configuration.acidity.configuration module seapopym.configuration.acidity.forcing_parameter module seapopym.configuration.acidity.functional_group_parameter module seapopym.configuration.no_transport module seapopym.configuration.no_transport.configuration module seapopym.configuration.no_transport.forcing_parameter module seapopym.configuration.no_transport.functional_group_parameter module seapopym.configuration.no_transport.kernel_parameter module seapopym.core module seapopym.core.kernel module seapopym.core.template module seapopym.function module seapopym.function.apply_coefficient_to_primary_production module seapopym.function.apply_mask_to_state module seapopym.function.average_acidity module seapopym.function.average_temperature module seapopym.function.biomass module seapopym.function.cell_area module seapopym.function.compiled_functions module seapopym.function.compiled_functions.biomass_compiled_functions module seapopym.function.compiled_functions.production_compiled_functions module

seapopym.function.day_length module seapopym.function.global_mask module seapopym.function.limits module seapopym.function.mask_by_functional_group module seapopym.function.mask_temperature module seapopym.function.min_temperature module seapopym.function.mortality_acidity_field module seapopym.function.mortality_field module seapopym.function.production module seapopym.model module seapopym.model.acidity_model module seapopym.model.no_transport_model module seapopym.standard module seapopym.standard.attributs module seapopym.standard.coordinates module seapopym.standard.labels module seapopym.standard.types module seapopym.standard.units module standard_name (seapopym.standard.labels.SeaLayers property) StandardUnitsLabels (class in seapopym.standard.units) StandardUnitsRegistry (class in seapopym.standard) (class in seapopym.standard.units) state (seapopym.configuration.no_transport.configuration.NoTransportConfiguration property) (seapopym.model.no_transport_model.NoTransportModel attribute) (seapopym.standard.ConfigurationProtocol property) (seapopym.standard.ModelProtocol attribute) survival_rate (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) survival_rate_0 (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute)

T

T (seapopym.configuration.no_transport.forcing_parameter.ChunkParameter attribute) temperature (seapopym.configuration.no_transport.forcing_parameter.ForcingParameter attribute) (seapopym.standard.ForcingLabels attribute) (seapopym.standard.labels.ForcingLabels attribute) (seapopym.standard.units.StandardUnitsLabels attribute) Template (class in seapopym.core.template) template (seapopym.core.kernel.KernelUnit attribute) (seapopym.model.no_transport_model.NoTransportModel property) template() (seapopym.core.kernel.Kernel method) template_unit (seapopym.core.template.Template attribute) template_unit_factory() (in module seapopym.core.template) TemplateProtocol (class in seapopym.standard) TemplateUnit (class in seapopym.core.template) time (seapopym.standard.CoordinatesLabels attribute) (seapopym.standard.labels.CoordinatesLabels attribute) (seapopym.standard.units.StandardUnitsLabels attribute)

timestep (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) timesteps_number (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute) to_dataset() (seapopym.configuration.no_transport.forcing_parameter.ForcingParameter method) (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupParameter method) (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit method) (seapopym.configuration.no_transport.kernel_parameter.KernelParameter method) (seapopym.standard.ForcingParameterProtocol method) (seapopym.standard.FunctionalGroupParameterProtocol method) to_remove_from_state (seapopym.core.kernel.KernelUnit attribute) tr_0 (seapopym.configuration.no_transport.functional_group_parameter.FunctionalTypeParameter attribute) (seapopym.standard.ConfigurationLabels attribute) (seapopym.standard.labels.ConfigurationLabels attribute)

U

units (seapopym.standard.units.StandardUnitsLabels property)

update_cohort_timestep() (seapopym.configuration.no_transport.functional_group_parameter.FunctionalGroupUnit method) UPMESO (seapopym.standard.labels.SeaLayers attribute)

V

validate_coordinates() (seapopym.standard.CoordinateAuthority method)

validate_unit_compatibility() (seapopym.standard.StandardUnitsRegistry static method) (seapopym.standard.units.StandardUnitsRegistry static method)

W

weight (seapopym.standard.units.StandardUnitsLabels attribute)

X

X (seapopym.configuration.no_transport.forcing_parameter.ChunkParameter attribute) (seapopym.standard.CoordinatesLabels attribute) (seapopym.standard.labels.CoordinatesLabels attribute)

Y

Y (seapopym.configuration.no_transport.forcing_parameter.ChunkParameter attribute) (seapopym.standard.CoordinatesLabels attribute) (seapopym.standard.labels.CoordinatesLabels attribute)

Z

Z (seapopym.standard.CoordinatesLabels attribute) (seapopym.standard.labels.CoordinatesLabels attribute)