To access the set of parameter included in Atlantis as of version 3-6722, use:
# only version 3-6722 is available
atl <- list_atlantis_parameters(version = "3-6722")
atl$meta[1:3]
#> $atlantis_source
#> [1] "AtlantisTrunk/atlantis"
#>
#> $atlantis_version
#> [1] 3.6722
#>
#> $bm_struct
#> [1] "MSEBoxModel"
atl$parameters[1:2]
#> [[1]]
#> [[1]]$name
#> [1] "include_atmosphere"
#>
#> [[1]]$description
#> [1] "Switch enabling the atmospheric exchange concentrations block"
#>
#> [[1]]$source_file
#> [1] "physics_prm"
#>
#> [[1]]$value_type
#> [1] "int"
#>
#> [[1]]$dimension
#> [1] "scalar"
#>
#> [[1]]$units
#> NULL
#>
#> [[1]]$bm_member
#> [1] "bm->include_atmosphere"
#>
#> [[1]]$reader
#> [[1]]$reader$fn
#> [1] "readkeyprm_i"
#>
#> [[1]]$reader$at
#> [1] "atphysics/atphysics.c:229"
#>
#> [[1]]$reader$check
#> [1] "none"
#>
#>
#> [[1]]$conditional_on
#> NULL
#>
#>
#> [[2]]
#> [[2]]$name
#> [1] "atmospheric_NH"
#>
#> [[2]]$description
#> [1] "Atmospheric ammonia concentration"
#>
#> [[2]]$source_file
#> [1] "physics_prm"
#>
#> [[2]]$value_type
#> [1] "double"
#>
#> [[2]]$dimension
#> [1] "scalar"
#>
#> [[2]]$units
#> [1] "mg N m-3"
#>
#> [[2]]$bm_member
#> [1] "bm->atmospheric_NH"
#>
#> [[2]]$reader
#> [[2]]$reader$fn
#> [1] "readkeyprm_d"
#>
#> [[2]]$reader$at
#> [1] "atphysics/atphysics.c:233"
#>
#> [[2]]$reader$check
#> [1] "none"
#>
#>
#> [[2]]$conditional_on
#> [1] "bm->include_atmosphere"The table below display the entire set of parameters, note that the
followwing abbreviations are used: -
Biology parameters
Biology
| Name | Description | Units | Type | Dimension |
|---|---|---|---|---|
| ecotest | Ecology test/diagnostic verbosity flag | int | scalar | |
| availflag | Switch controlling how prey availability is interpreted | int | scalar | |
| flagrandom | Enable stochastic/random processes | int | scalar | |
| readin_popratio | Read population ratio (stock) data flag | int | scalar | |
| flagresp | Respiration submodel flag | int | scalar | |
| flagavgmig | Average migration flag | int | scalar | |
| flagbactstim | Bacterial stimulation flag | int | scalar | |
| flagtrackpops | Track populations flag | int | scalar | |
| flagseason | Seasonal forcing flag | int | scalar | |
| flaglight | Light limitation model flag | int | scalar | |
| flaglightopt | Light optimisation option | int | scalar | |
| lim_sun_hours | Limit primary production to daylight hours flag | int | scalar | |
| flagmodeltemp | Temperature dependence model flag | int | scalar | |
| flagq10 | Global Q10 temperature scaling flag | int | scalar | |
| O2case | Oxygen limitation case selector | int | scalar | |
| flagnut | Nutrient limitation flag | int | scalar | |
| flagmicro | Microbial loop flag | int | scalar | |
| flagtempchange | Apply prescribed temperature change flag | int | scalar | |
| flagsaltchange | Apply prescribed salinity change flag | int | scalar | |
| flagpHchange | Apply prescribed pH change flag | int | scalar | |
| flagstarve | Starvation mortality flag | int | scalar | |
| flagdegrade | Detritus degradation flag | int | scalar | |
| flagroc | Rate-of-change effects flag | int | scalar | |
| flaghomog_sp | Homogeneous spatial distribution flag | int | scalar | |
| flagagestruct | Age structure global flag | int | scalar | |
| flagsenesce | Senescence mortality flag | int | scalar | |
| flagtsforcerecruit | Time-series forced recruitment flag | int | scalar | |
| flag_modify_KWSR | Modify weight-at-spawn ratio flag | int | scalar | |
| flag_extpop_growth_option | External population growth option | int | scalar | |
| juv_transition_thresh | Juvenile-to-adult size transition threshold | double | scalar | |
| mat_transition_thresh | Maturity transition threshold | double | scalar | |
| norm_larval_distrib | Normalise larval distribution flag | int | scalar | |
| larvae_connect_only | Larvae connectivity-only flag | int | scalar | |
| enviro_independ_larvae | Environment-independent larvae flag | int | scalar | |
| flag_recruit_effect | Recruitment environmental effect flag | int | scalar | |
| flag_macro_model | Macrophyte/seagrass model flag | int | scalar | |
| flag_benthos_sediment_link | Benthos-sediment coupling flag | int | scalar | |
| flag_competing_epiff | Competing epibenthic filter feeders flag | int | scalar | |
| max_available_habitat | Maximum available habitat fraction | double | scalar | |
| flag_invert_biohab | Invertebrate biogenic habitat flag | int | scalar | |
| flag_olddiet | Use legacy diet handling flag | int | scalar | |
| flag_fine_ontogenetic_diets | Fine-grained per-age diet matrices flag | int | scalar | |
| UseHardFeedingWindow | Use hard (step) feeding window flag | int | scalar | |
| UseBiLogisticFeedingWindow | Use bi-logistic feeding window flag | int | scalar | |
| flag_satiation | Predator satiation flag | int | scalar | |
| flag_shrinkfat | Allow shrinking/fat loss flag | int | scalar | |
| flag_predratiodepend | Ratio-dependent predation flag | int | scalar | |
| flag_dynamicXRS | Dynamic reserve/structural ratio flag | int | scalar | |
| flag_repcostSpawn | Reproduction cost at spawning flag | int | scalar | |
| flag_lengthSN | Length from structural N flag | int | scalar | |
| XRS_cap | Cap on reserve-to-structural ratio | double | scalar | |
| flag_rel_cover | Relative cover model flag | int | scalar | |
| flag_report_water_detritus | Report water-column detritus flag | int | scalar | |
| flag_refuge_model | Prey refuge model flag | int | scalar | |
| flag_rugosity_model | Rugosity model flag | int | scalar | |
| flag_georugosity | Geological (background) rugosity flag | int | scalar | |
| RugCover_Coefft | Rugosity-cover relationship coefficient | double | scalar | |
| RugCover_Const | Rugosity-cover relationship constant | double | scalar | |
| RugCover_Cap | Rugosity-cover relationship cap | double | scalar | |
| min_rugosity | Minimum rugosity | double | scalar | |
| max_rugosity | Maximum rugosity | double | scalar | |
| rugosity_const | Rugosity baseline constant | double | scalar | |
| rugosity_bozec_a | Bozec rugosity model coefficient a | double | scalar | |
| rugosity_bozec_b | Bozec rugosity model coefficient b | double | scalar | |
| rugosity_bozec_c | Bozec rugosity model coefficient c | double | scalar | |
| rugosity_bozec_d | Bozec rugosity model coefficient d | double | scalar | |
| flagmodelpH | pH dynamics model flag | int | scalar | |
| pH_sensitivity_model | pH sensitivity model selector | int | scalar | |
| flagPHmortcase | pH mortality case selector | int | scalar | |
| pH_surface_depth | Surface pH layer depth boundary | m | double | scalar |
| pH_mid_depth | Mid pH layer depth boundary | m | double | scalar |
| pH_surface_coefft_T | Surface pH regression coefficient on temperature | double | scalar | |
| pH_surface_coefft_S | Surface pH regression coefficient on salinity | double | scalar | |
| pH_surface_coefft_O | Surface pH regression coefficient on oxygen | double | scalar | |
| pH_surface_const | Surface pH regression constant | double | scalar | |
| pH_mid_coefft_T | Mid-layer pH regression coefficient on temperature | double | scalar | |
| pH_mid_coefft_S | Mid-layer pH regression coefficient on salinity | double | scalar | |
| pH_mid_coefft_O | Mid-layer pH regression coefficient on oxygen | double | scalar | |
| pH_mid_const | Mid-layer pH regression constant | double | scalar | |
| pH_deep_coefft_T | Deep-layer pH regression coefficient on temperature | double | scalar | |
| pH_deep_coefft_S | Deep-layer pH regression coefficient on salinity | double | scalar | |
| pH_deep_coefft_O | Deep-layer pH regression coefficient on oxygen | double | scalar | |
| pH_deep_const | Deep-layer pH regression constant | double | scalar | |
| flagmodelArag | Aragonite saturation model flag | int | scalar | |
| K_max_num_DHW | Max number of degree heating weeks records | int | scalar | |
| Karag_A | Aragonite regression coefficient A | double | scalar | |
| Karag_B | Aragonite regression coefficient B | double | scalar | |
| Karag_C | Aragonite regression coefficient C | double | scalar | |
| Karag_pH | Aragonite regression coefficient on pH | double | scalar | |
| Kca_const | Calcium constant for calcification | double | scalar | |
| K_Ks | Calcification saturation half-constant | double | scalar | |
| Ksmother_coefft | Smothering coefficient | double | scalar | |
| Ksmother_const | Smothering constant | double | scalar | |
| Pads_r_t0 | Phosphate adsorption rate at reference temp | double | scalar | |
| Pads_K | Phosphate adsorption half-saturation | double | scalar | |
| Pads_KO | Phosphate adsorption oxygen dependence | double | scalar | |
| r_immob_PIP_t0 | Particulate inorganic P immobilisation rate at reference temp | double | scalar | |
| Enviro_turb | Environmental turbidity switch | int | scalar | |
| K_TUR | Turbidity half-saturation | double | scalar | |
| K_TUR_DEP | Turbidity depth dependence | double | scalar | |
| K_MAX_TUR | Maximum turbidity | double | scalar | |
| K_IRR | Irradiance half-saturation | double | scalar | |
| K_MAX_IRR | Maximum irradiance | double | scalar | |
| K_MIN_IRR | Minimum irradiance | double | scalar | |
| r_DC_T15 | Labile detritus carbon breakdown rate at 15C | d-1 | double | scalar |
| r_DL_T15 | Labile detritus breakdown rate at 15C | d-1 | double | scalar |
| r_DR_T15 | Refractory detritus breakdown rate at 15C | d-1 | double | scalar |
| r_DON_T15 | Dissolved organic N breakdown rate at 15C | d-1 | double | scalar |
| r_DSi_T15 | Dissolved silica regeneration rate at 15C | d-1 | double | scalar |
| FDR_DC | Fraction of refractory detritus to DC | double | scalar | |
| FDR_DL | Fraction of refractory detritus to DL | double | scalar | |
| FDON_D | Fraction of detritus to DON | double | scalar | |
| R_0_T15 | Base remineralisation rate at 15C | d-1 | double | scalar |
| R_D_T15 | Detritus remineralisation rate at 15C | d-1 | double | scalar |
| Dmax | Maximum depth for remineralisation | m | double | scalar |
| K_nit_T15 | Nitrification rate at 15C | d-1 | double | scalar |
| K_conc | Nitrification concentration half-saturation | double | scalar | |
| p_NH_anad | Proportion NH from anaerobic decomposition | double | scalar | |
| X_ON | Oxygen-to-nitrogen Redfield ratio | double | scalar | |
| X_CN | Carbon-to-nitrogen Redfield ratio | double | scalar | |
| X_CHLN | Chlorophyll-to-nitrogen ratio | double | scalar | |
| X_SiN | Silica-to-nitrogen ratio | double | scalar | |
| X_FeN | Iron-to-nitrogen ratio | double | scalar | |
| k_wetdry | Wet/dry weight conversion factor | double | scalar | |
| k_w_cdepth | Light attenuation coefficient at critical depth | m-1 | double | scalar |
| k_w_depth | Light attenuation coefficient with depth | m-1 | double | scalar |
| k_w_deep | Deep-water light attenuation coefficient | m-1 | double | scalar |
| k_w_shallow | Shallow-water light attenuation coefficient | m-1 | double | scalar |
| k_PN | Light attenuation per unit particulate N | double | scalar | |
| k_DON | Light attenuation per unit DON | double | scalar | |
| k_DL | Light attenuation per unit labile detritus | double | scalar | |
| k_IS | Light attenuation per unit inorganic suspended matter | double | scalar | |
| k_SED | Light attenuation per unit sediment | double | scalar | |
| KIOP_min | Minimum I-optimal half-saturation | double | scalar | |
| KIOP_shift | I-optimal shift parameter | double | scalar | |
| KI_avail | Irradiance availability scalar | double | scalar | |
| K_addepth | Additional depth offset for light calc | m | double | scalar |
| swr_scalar | Shortwave radiation scaling factor | double | scalar | |
| swr_const | Shortwave radiation constant | double | scalar | |
| swr_cos_coefft | Shortwave radiation seasonal cosine coefficient | double | scalar | |
| swr_cos_offset | Shortwave radiation seasonal cosine offset | double | scalar | |
| albedo_ice | Ice albedo | double | scalar | |
| k_bs | Light attenuation under bare snow | double | scalar | |
| k_bi | Light attenuation under bare ice | double | scalar | |
| k_rs | Light attenuation under refrozen snow | double | scalar | |
| k_ri | Light attenuation under refrozen ice | double | scalar | |
| R_bi | Reflectance of bare ice | double | scalar | |
| k_ice | Light attenuation coefficient for ice | m-1 | double | scalar |
| ka_star | Specific light absorption coefficient | double | scalar | |
| Tchange_max_num | Number of prescribed temperature-change records | int | scalar | |
| Tchange | Prescribed temperature-change time-series (value/time pairs) | degC | double_array | timeseries |
| Schange_max_num | Number of prescribed salinity-change records | int | scalar | |
| Schange | Prescribed salinity-change time-series | double_array | timeseries | |
| pHchange_max_num | Number of prescribed pH-change records | int | scalar | |
| PHchange | Prescribed pH-change time-series | double_array | timeseries | |
| RTOP | Top of refuge tolerance | double | scalar | |
| K_Lc | Critical light constant | double | scalar | |
| RelTol | Relative numerical tolerance | double | scalar | |
| Flux_tol | Flux tolerance threshold | double | scalar | |
| min_pool | Minimum tracer pool concentration | double | scalar | |
| min_dens | Minimum density threshold | double | scalar | |
| min_channel_depth | Minimum channel depth | m | double | scalar |
| flag_do_var_express | Variable expression flag (evolution) | int | scalar | |
| flag_do_evolution | Enable evolution module | int | scalar | |
| flag_bound_change | Allow trait bound change flag | int | scalar | |
| flag_inheritance | Trait inheritance flag | int | scalar | |
| flag_evolvar_capped | Cap evolved variance flag | int | scalar | |
| evol_stdev_range | Evolutionary standard deviation range | double | scalar | |
| max_rate_evol | Maximum rate of evolutionary change | double | scalar | |
| flag_mult_grow_curves | Multiple growth morph curves flag | int | scalar | |
| ActiveTrait/<GRP> | Per-group active evolutionary trait flags (one row of trait toggles per group) | double_array | per_group | |
| MB_wc | Microbial biomass water-column reference | double | scalar | |
| eddy_scale | Eddy diffusivity scaling for PP | double | scalar | |
| XPB_DL | Fraction of PB flux to labile detritus | double | scalar | |
| XBB_DL | Fraction of BB flux to labile detritus | double | scalar | |
| XPB_DR | Fraction of PB flux to refractory detritus | double | scalar | |
| XBB_DR | Fraction of BB flux to refractory detritus | double | scalar | |
| k_PB | Pelagic bacteria rate constant | double | scalar | |
| k_BB | Benthic bacteria rate constant | double | scalar | |
| flaghabdepend | Habitat-dependent processes flag | int | scalar | |
| flag_move_habdepend | Habitat-dependent movement flag | int | scalar | |
| flagenviro_displace | Environmental displacement flag | int | scalar | |
| flagenviro_kill | Environmental kill flag | int | scalar | |
| REEFchange_max_num | Number of reef-cover change records | int | scalar | |
| FLATchange_max_num | Number of flat-cover change records | int | scalar | |
| SOFTchange_max_num | Number of soft-cover change records | int | scalar | |
| REEFchange | Reef-substrate cover change time-series | double_array | timeseries | |
| FLATchange | Flat-substrate cover change time-series | double_array | timeseries | |
| SOFTchange | Soft-substrate cover change time-series | double_array | timeseries | |
| Group_Habitat_Preference/<GRP> | Per-group habitat preference array over habitat types | double_array | per_group | |
| Group_Ice_Preference/<GRP> | Per-group ice habitat preference array | double_array | per_group | |
| Group_IceReprod_Preference/<GRP> | Per-group ice reproduction preference array | double_array | per_group | |
| roc_wgt | Rate-of-change weighting | double | scalar | |
| k_roc_food | Rate-of-change food scaling constant | double | scalar | |
| flagtempdepend_move | Temperature-dependent movement flag | int | scalar | |
| flagtempdepend_reprod | Temperature-dependent reproduction flag | int | scalar | |
| flagsaltdepend | Salinity-dependent processes flag | int | scalar | |
| flagO2depend | Oxygen-dependent processes flag | int | scalar | |
| flagconstrain_epiwander | Constrain epibenthic wandering flag | int | scalar | |
| X_RS | Reserve-to-structural target ratio | double | scalar | |
| Kthresh1 | Movement/feeding threshold constant 1 (read twice; two threshold slots) | double | scalar | |
| KHTD | Habitat threshold constant (deep) | double | scalar | |
| KHTI | Habitat threshold constant (intertidal) | double | scalar | |
| SeasonalDistribution/<GRP>/<STAGE> | Per-group/per-stage seasonal horizontal distribution (juvenile/adult, per box) | double_array | per_box | |
| p_BBfish | Proportion bacteria cleaned from fish-ingested detritus | double | scalar | |
| p_BBben | Proportion bacteria cleaned from benthic-ingested detritus | double | scalar | |
| p_PBwc | Proportion of pelagic bacteria available in water column | double | scalar | |
| p_PBben | Proportion of pelagic bacteria available in benthos | double | scalar | |
| k_refDL | Reference labile-detritus level for omnivore supplement feeding | double | scalar | |
| k_refDR | Reference refractory-detritus level for supplement feeding | double | scalar | |
| k_refsDL | Reference sediment labile-detritus level | double | scalar | |
| flagfishrates | Use fish-specific clearance/growth rates flag | int | scalar | |
| li_a_invert | Length-weight allometry coefficient a for invertebrates | double | scalar | |
| li_b_invert | Length-weight allometry exponent b for invertebrates | double | scalar | |
| pPREY<PREDCOHORT><PRED><PREYCOHORT> | Vertebrate predator-prey availability matrix (pSPVERTeat), availability of each prey group to a predator age class | double_array | per_prey | |
| pPREY<PRED> | Invertebrate/biomass-pool predator-prey availability row (single cohort) | double_array | per_prey | |
| DetritusSedimentFoodAvail/<GRP>[/<COHORT>] | Availability of detritus/sediment groups to a predator (per detritus group, per cohort for age-structured) | double_array | per_prey | |
| AgeDietAvail/<GRP> | Fine ontogenetic (per-age) prey availability matrix | double_array | per_prey | |
| SeagrassFoodAvail/<GRP> | Availability of seagrass/macrophyte parts to grazers | double_array | per_prey | |
| Supplemental_Diets/<GRP> | Imported/supplemental feed distribution per box for cultured/supplemented groups | double_array | per_box | |
| Catch_Opportunity/Catch_Availability/<GRP> | Availability of fishery catch to opportunistic catch-eaters (per prey group) | double_array | per_prey | |
| Catch_Opportunity/Proportion_Exploitable/<GRP> | Proportion of each fishery’s catch exploitable by catch-eaters | double_array | other | |
| C_<GRP> | Per-cohort vertebrate clearance (search-volume) rate; prm key C_<GRP> array over age classes | m3 (mg N)-1 d-1 | double_array | per_cohort |
| C_<GRP>_T15 | Invertebrate grazer clearance rate at 15C; scalar per group | m3 (mg N)-1 d-1 | double | per_group |
| mum_<GRP> | Per-cohort vertebrate maximum growth (consumption) rate; prm key mum_<GRP> array over age classes | mg N d-1 (per individual) | double_array | per_cohort |
| mum_<GRP>_T15 | Invertebrate/PP/bacteria maximum growth rate at 15C; scalar per group | d-1 | double | per_group |
| InvertebrateSN/<GRP> | Invertebrate structural-N (size) reference per group | mg N | double_array | per_group |
| Q10 | Global Q10 temperature scaling factor | double | scalar | |
| temp_coefftB | Temperature response coefficient B | double | scalar | |
| temp_coefftC | Temperature response coefficient C | double | scalar | |
| temp_exp | Temperature response exponent | double | scalar | |
| KST_fish | Standard metabolic temperature scalar - fish | double | scalar | |
| KST_shark | Standard metabolic temperature scalar - shark | double | scalar | |
| KST_bird | Standard metabolic temperature scalar - bird | double | scalar | |
| KST_mammal | Standard metabolic temperature scalar - mammal | double | scalar | |
| Ktmp_fish | Temperature respiration coefficient - fish | double | scalar | |
| Ktmp_shark | Temperature respiration coefficient - shark | double | scalar | |
| Ktmp_bird | Temperature respiration coefficient - bird | double | scalar | |
| Ktmp_mammal | Temperature respiration coefficient - mammal | double | scalar | |
| Kthreshm | Mortality threshold constant | double | scalar | |
| FFDDR | Fraction of feeding-derived detritus going to refractory pool | double | scalar | |
| FDL_fish | Fraction labile detritus from fish mortality | double | scalar | |
| FDL_benth | Fraction labile detritus from benthic invert mortality | double | scalar | |
| FDL_top | Fraction labile detritus from top predator mortality | double | scalar | |
| FDL_wc | Fraction labile detritus from water-column group mortality | double | scalar | |
| FDL_SG_roots | Fraction labile detritus from seagrass roots | double | scalar | |
| FDL_SG_leaves | Fraction labile detritus from seagrass leaves | double | scalar | |
| FPB_DR | Fraction pelagic-bacteria flux to refractory detritus | double | scalar | |
| FBB_DR | Fraction benthic-bacteria flux to refractory detritus | double | scalar | |
| FPB_DON | Fraction pelagic-bacteria flux to DON | double | scalar | |
| FBB_DON | Fraction benthic-bacteria flux to DON | double | scalar | |
| Fben_den | Fraction benthic denitrification | double | scalar | |
| ImplicitSeabirdMortalityRate/<GRP> | Implicit (external) seabird mortality rate per group | d-1 | double_array | per_group |
| ImplicitFishMortalityRate/<GRP> | Implicit (external) fish mortality rate per group | d-1 | double_array | per_group |
| flagtrecruitdistrib | Time-varying recruit distribution flag | int | scalar | |
| recover_trigger | Population recovery trigger level | double | scalar | |
| recover_span | Recovery span duration | double | scalar | |
| recover_subseq | Subsequent recovery parameter | double | scalar | |
| lognorm_mu | Lognormal recruitment mean parameter | double | scalar | |
| lognorm_sigma | Lognormal recruitment standard deviation parameter | double | scalar | |
| rec_m | Recruitment mean (stochastic) parameter | double | scalar | |
| rec_sigma | Recruitment standard deviation parameter | double | scalar | |
| recruitRange | Recruitment search range | double | scalar | |
| recruitRangeFlat | Flat recruitment range | double | scalar | |
| ref_chl | Reference chlorophyll for recruitment effect | double | scalar | |
| FSPB_<GRP> | Per-cohort proportion of spawning biomass; prm key FSPB_<GRP> array over age classes | double_array | per_cohort | |
| KDENR_<GRP> | Per-cohort density-dependent recruitment parameter (Reproduction/KDENR) | double_array | per_cohort | |
| recSTOCK_<GRP> | Per-stock recruitment allocation (Reproduction/recSTOCK) | double_array | other | |
| popratioStock_<GRP> | Per-stock population ratio at initialisation (Reproduction/popratioStock) | double_array | other | |
| pStock_<GRP> | Per-stock diet/spatial proportion (Diet/pStock) | double_array | other | |
| VerticalRecruitLocation/<GRP> | Per-group vertical layer distribution for recruits | double_array | per_layer | |
| RecruitDistribution/<GRP> | Per-group horizontal recruit distribution over boxes | double_array | per_box | |
| AquacultDistribution/<GRP> | Per-group horizontal aquaculture stocking distribution over boxes | double_array | per_box | |
| <GRP>_Time_Spawn | Per-spawn-event spawning time-of-year per group (prm key *_Time_Spawn) | day-of-year | int_array | per_cohort |
| Time_Age_<GRP> | Per-event time-to-age cohort entry per group (prm key Time_Age_<GRP>) | day | int_array | per_cohort |
| StockStructure/<GRP> | Per-group per-box stock membership (integer stock id per box) | int_array | per_box | |
| VerticalStockStructure/<GRP> | Per-group per-layer vertical stock membership | int_array | per_layer | |
| invading_sp_model | Invading-species model flag | int | scalar | |
| InvaderIndex | Functional-group index of the invader | int | scalar | |
| minInvaderAge | Minimum age of invading individuals | int | scalar | |
| maxInvaderAge | Maximum age of invading individuals | int | scalar | |
| InvaderEntryBox | Box index where invader enters | int | scalar | |
| InvadersEntering | Number of invaders entering | double | scalar | |
| InvaderMinDepth | Minimum entry depth for invader | m | double | scalar |
| InvaderMaxDepth | Maximum entry depth for invader | m | double | scalar |
| InvaderStartDay | Day-of-year invasion starts | day-of-year | int | scalar |
| InvaderEndDay | Day-of-year invasion ends | day-of-year | int | scalar |
| InvaderScalar | Scaling of invader numbers | double | scalar | |
| InvaderSpeed | Invader movement speed | double | scalar | |
| InvaderEntryLayer | Vertical layer of invader entry | int | scalar | |
| p_IBice | Proportion of biota associated with ice | double | scalar | |
| flag_dissolved_pollutants | Track dissolved pollutants flag | int | scalar | |
| flag_contamMortModel | Contaminant mortality model flag | int | scalar | |
| flag_contamInteractModel | Contaminant interaction model flag | int | scalar | |
| flag_contamGrowthModel | Contaminant growth-effect model flag | int | scalar | |
| flag_contamReprodModel | Contaminant reproduction-effect model flag | int | scalar | |
| flag_contamOnlyAmplify | Contaminant amplify-only flag | int | scalar | |
| flag_contamMove | Contaminant movement flag | int | scalar | |
| flag_contamMinTemp | Contaminant minimum-temperature flag | int | scalar | |
| flag_contam_halflife_spbased | Species-based contaminant half-life flag | int | scalar | |
| flag_contamMaternalTransfer | Maternal contaminant transfer flag | int | scalar | |
| flag_contam_distrib | Contaminant distribution flag | int | scalar | |
| biopools_dodge_contam | Biological pools bypass contaminant flag | int | scalar | |
| min_pool_cont | Minimum contaminant pool concentration | double | scalar | |
| contam_tau | Contaminant decay time constant | double | scalar | |
| contam_sig_uptake_const | Contaminant sigmoidal uptake constant | double | scalar | |
| flag_detritus_contam | Detritus contaminant tracking flag | int | scalar | |
| k_migslow | Migration slowdown constant | double | scalar | |
| Migration/MigrateIOBox/<GRP>[/<COHORT>]/Migrate<N> | Per-migration destination box proportions for migrating groups | double_array | per_box | |
| Migration/KMIG_DEN/<GRP> | Initial density of pre-existing out-of-model migrators | double_array | per_cohort | |
| Migration/KMIG_RN/<GRP> | Initial reserve N of pre-existing out-of-model migrators | mg N | double_array | per_cohort |
| Migration/KMIG_SN/<GRP> | Initial structural N of pre-existing out-of-model migrators | mg N | double_array | per_cohort |
| Migration/KMIG_INVERT<N>/<GRP> | Initial density of out-of-model invertebrate migrators per migration | double_array | per_cohort | |
| flag<GRP> | Group functioning (on/off) flag | int | per_group | |
| flagdem<GRP> | Preferred-location (demersal) trend flag | int | per_group | |
| flagplankfish<GRP> | Planktivore flag | int | per_group | |
| <GRP>thresh | Flux threshold for sediment/bacteria flux | double | per_group | |
| <GRP>damp | Flux damping coefficient | double | per_group | |
| SPECIES_FAMILY Reproduction_flags | Per-group reproduction flags and parameters. One entry each, prm key = base_GRP: flagbearlive (live-bearing), feed_while_spawn, flagmother (parental care), flagrecruit (recruitment function id), flagrecpeak, flagstocking, flagkeep_plusgroup, Recruit_Period, Recruit_Time, cohort_recruit_entry, spawn_period, KSPA (spawn area), FSP (spawn fraction), Kcov_juv/Bcov_juv_/Acov_juv_/Kcov_ad_/Bcov_ad_/Acov_ad_ (cover coeffts), RugCover_scalar, age_mat (age at maturity), recover_start, KWSR, KWRR_, recover_mult_, BHbeta_/BHalpha_ (Beverton-Holt), Rbeta_/Ralpha_ (Ricker), PP_ (constant recruits), log_mult, norm_sigma, flag_recruit_stochastic, prod_alpha, den_depend_beta1/beta2, temp_coefft_, rate_coefft_, wind_coefft_, rec_var_, min/max_spawn_temp, min/max_spawn_salt, prop_spawn_lost, jack_a/jack_b_, rec_HabDepend, intersp_depend_recruit_/sp_/scale_, aquacult_fry, KA_/KB_ (weight-length). | varies | double | per_group |
| overwinterStartTofY_<GRP> | Overwinter start time-of-year (encystment block) | day-of-year | double | per_group |
| SPECIES_FAMILY Overwinter_Encystment | Per-group overwintering/encystment params: overwinterStartTofY_, overwinterEndTofY_, overwinterStartTemp_, overwinterEndTemp_, crit_mum_, crit_nut_, crit_temp_, encyst_rate_, hatch_rate_, encyst_period_, flagencyst_. | varies | double | per_group |
| SPECIES_FAMILY Evolution | Per-group evolution params: max_prop_shift_, inheritance_, trait_variance_, min_trait_variance_. | double | per_group | |
| SPECIES_FAMILY FeedingDetritusFractions | Per-group fractions of feeding-derived material to detritus: FDM_<GRP> (mortality detritus), FDG_<GRP> (egesta), FDGDL_, FDGDR_. | double | per_group | |
| SPECIES_FAMILY FeedingDynamics | Per-group/predator feeding parameters: catcheater, flagactiveDAY (diel activity), vla<GRP>T15 (assimilation), KL<GRP>/KU_<GRP>/KUP_<GRP>/KLP_<GRP> (feeding window lower/upper), Kmax_coefft_<GRP>, KDEP_<GRP> (sediment penetration depth), vlb_, hta_, htb_ (handling time), pR_ (reserve proportion fed), li_a_/li_b_/linf_/Kbert_/tzero_ (length-at-age, VB), min_li_mat_, predcase (functional response type), age_structured_prey_, p_split_, extra_feed, vl<GRP> (invert search volume), ht_ (invert handling time), hvm_, turbid_refuge_, RSmax_/RSmid_/RSslope_/RSprop_/SNcost_/RNcost_/RSstarve_ (reserve dynamics), E_<GRP>/EPlant_<GRP>/EDL_<GRP>/EDR_<GRP> (assimilation efficiencies on prey/plant/labile/refractory). | varies | double | per_group |
| SPECIES_FAMILY Q10_Temperature | Per-group temperature response: flagq10eff, flagq10receff, q10_<GRP>, q10_method_, q10_optimal_temp_, q10_correction_, temp_coefftA_, flagtempsensitive, flagfecundsensitive. | double | per_group | |
| SPECIES_FAMILY Salinity_pH_sensitivity | Per-group salinity/pH sensitivity: flagSaltSensitive, salt_correction_, flagpHsensitive, pHsensitive_model_, pH_constA_/B_/C_, min_pH_/max_pH_, KN_pH_, optimal_pH_, pH_correction_, contract_tol_, flagcontract_tol_, flagpredavaileffect, flagnutvaleffect, pHmortstart_, pHmortA_/B_, pHmortmid_. | double | per_group | |
| SPECIES_FAMILY Pollution_impact | Per-group pollution light/noise sensitivity coefficients: light_coefft_, noise_coefft_. | double | per_group | |
| SPECIES_FAMILY PrimaryProducer_uptake | Per-PP/seagrass parameters: KTUR_ (bioturbation), KIRR_ (infauna irradiance), KN_ (DIN half-sat), KS_ (Si half-sat), KF_ (Fe half-sat), flag*lim, KI_<GRP>T15 (light half-sat), L_KI<GRP>T15 (seagrass leaf light), Kext/Ksub_/KN_epi_/KsubEpi_/Ktrans_ (seagrass), Beta_D_, PBmax_D_, P_uptake_/P_scale_uptake_/P_concp_/P_min_internal_/P_max_internal_, C_uptake_/C_scale_uptake_/C_concp_, PSA_min_/C_min_, Phyto_Resp_Rate_, KP_ (P half-sat), KLYS_ (lysis rate), FSBDR_. | varies | double | per_group |
| SPECIES_FAMILY Mortality | Per-group/per-cohort mortality rates at 15C: mQ (quadratic), mL (linear), mLext (external linear), mPext (external proportional); plus mS<GRP>T15 (macrophyte senescence), mStarve (starvation), mT (temperature mortality), mD (depth-oxygen), mO (oxygen), KO2_ (lethal O2), KO2LIM_ (limiting O2), turbidity mortality _turbid_L/_turbid_a/_turbid_b. The _mQ/_mL/_mLext/_mPext and turbidity entries are read per-cohort via Read_Cohort_Species_Param_Values; others via Util_XML_Read_Species_Param. | d-1 | double | per_cohort |
| SPECIES_FAMILY Physical_limits_movement | Per-group physical limitation and movement: low_/max_/sat_/thresh (basal/sed-FF feeding limits), _ddepend_move (movement model), _max/min_move_temp, _max/min_move_salt, _K_temp_const, K_salt_const, Speed, _mindepth/_maxdepth/_maxtotdepth, _min_O2, _K_o2_const, _homerangerad, _overlap, k_trans, _remin_contrib. | varies | double | per_group |
| SPECIES_FAMILY Coral_Sponge | Per-group coral/sponge params (bleaching, calcification, rugosity, smothering): _bleach_periodA/B, _mBleach, _bleaching_rate, _bleach_recovery_rate, _bleach_tempshift, _bleach_growshift, _bleach_temp, _min_bleach_temp, _prop_zooxanth, _DHW_thresh, _threshdepth, _depmum_scalar, _min/max_bleach_salt, _HostRemin, _calcifRefBaseline, _calcifTconst/Tcoefft/Topt/Lambda, _FeedLightThresh, _PropLightFeed, _coral_max_accel_trans/A/B, _CrecruitA/B/C, _coral_overgrow, _coral_compete, _sponge_overgrow, _sponge_compete, _Ksmother_A/B, _Vmax_deltaSi, _Km_deltaSi, _rug_erode, _rug_bleacherode, _rugFeedScalar, _rug_factor, _colony_ha, _rug_erode_sponge, _rugosity_inc/_rugosity_dec, _colony_diam. | varies | double | per_group |
| SPECIES_FAMILY Fishing_targetting | Per-group fishing/management flags read from bio prm: flagfish (targeting), flag_access_thru_wc_, age_harvest (aquaculture), tier (HCR tier), regionalSP, basketSP, basket_size, max_co_sp, coType_, tac_resetperiod, cpue_cdf_poor_r_/p_, cpue_cdf_top_r_/p_, samplesize, allometic li_a/li_b/li_bin/li_start/li_max, R_max, avg_inv_size, flag_assess, assess_bootstrap, assess_nat_mort, flag_prod_model, top_pcnt, bot_pcnt, assess_datastream, whichRAssess_, ICE_KDEP_. | varies | double | per_group |
| SPECIES_FAMILY RBC_assessment | Per-group reference-biomass-control / stock-assessment parameters (RBCSpeciesParamStructArray, atUtilXML.c:511-636): DiscType_, MaxH_, Growthage_L1_/L2_, MinCatch_, AssessStart_, NumRegions_, Nsexes_, Tier1/2/3Sig_, isTriggerSpecies_, trigger_threshold_, UseRBCAveraging_, Maturity_Inflect_/Slope_, T1_steep_phase_, tiertype_, Tier3_* (Fcalc/time/maxage/M/S25/S50/F/h/matlen/maxF), CCsel_years_, Tier4_* (avtime/CPUEyrmin/max/m/alpha/Cmaxmult/Bo_correct), Tier5_* (length/S50/cv/flt/reg/p/sel/q), PostRule_, CPUEmult_, MaxChange_, TriggerResponseScen_, MG_offset_, Regime_shift_assess_, RecDevBack_, Hsteep_, Agesel_Pattern_, AssessFreq_, BallParkF_/Yr_, NumChangeLambda_, num_enviro_obs_, num_growth_morphs_, Nsex_samp_, MaxAge_, Nyfuture_, NumFisheries_, Nlen_, Lbin_, thresh_mat_, femsexratio_, flagLAdirect_/SLAdirect_/WAdirect_, SigmaR1_/R2_/R_future_, PSigmaR1_, Regime_year_, RecDevMinYr_/MaxYr_, RecDevFlag_, AutoCorRecDev_, LFSSlim_, AFSSlim_, NumSurvey_, Regime_year_assess_, NblockPattern_, SRBlock_, assRecDevMinYear_, MultispAssessType_, mgt_indicator_, init_mgt_category_/sp_, PGMSYBHalpha_/beta_. | varies | double | per_group |
Groups
| Name | Description | Units | Type | Dimension |
|---|---|---|---|---|
| Code | 2-3 uppercase letter group code identifier | string | per_group | |
| Index | Row index of the group; read but discarded (ignored) | int | per_group | |
| IsTurnedOn | Whether the functional group is active/turned on | double | per_group | |
| Name | Short functional group name (used to build tracer names) | string | per_group | |
| LongName | Full/long functional group name | string | per_group | |
| NumCohorts | Number of cohorts (age classes) for the group | int | per_group | |
| NumGeneTypes | Number of genetic/phenotype types per cohort | int | per_group | |
| NumStages | Number of life stages (e.g. juvenile/adult) | int | per_group | |
| NumSpawns | Number of spawning events per year | int | per_group | |
| NumAgeClassSize | Number of years represented by each cohort (age class size) | years | int | per_group |
| NumStocks | Number of stocks per species | int | per_group | |
| VerticallyMigrates | Whether the group moves vertically in day-to-day movement (mapped to XML “VerticallyMobile”) | int | per_group | |
| HorizontallyMigrates | Whether the group moves horizontally in day-to-day movement (mapped to XML “Mobile”) | int | per_group | |
| NumMigrations | Number of migration entries/periods for the group | int | per_group | |
| MultiYrMigrations | Whether migrations span multiple years | int | per_group | |
| ExternalReproduction | Whether the group reproduces externally (outside the model domain) | int | per_group | |
| RecruitType | Recruitment relationship/option used for the group | int | per_group | |
| IsFished | Whether the group is subject to fishing | int | per_group | |
| IsImpacted | Whether the group is impacted by fishing/management | int | per_group | |
| isTAC | Whether the group is managed under a Total Allowable Catch (mapped to XML “IsTAC”) | int | per_group | |
| GroupType | Group type string (e.g. FISH, LG_PHY, LAB_DET) mapped to internal groupType enum | string | per_group | |
| IsPredator | Whether the group preys on other groups | int | per_group | |
| IsCover | Whether the group provides habitat cover (must be epibenthic) | int | per_group | |
| IsSiliconDep | Whether the group depends on silicon (e.g. diatoms) | int | per_group | |
| IsAssessed | Whether the group is stock-assessed (>1 enables close-kin) | int | per_group | |
| IsCatchGrazer | Whether the group grazes on catch/discards | double | per_group | |
| OverWinters | Whether the group overwinters (distinct overwintering distribution) | int | per_group | |
| isCultured | Whether the group is aquaculture-cultured | int | per_group | |
| isHabDepend | Whether the group is habitat dependent | int | per_group | |
| numMoveEntries | Number of seasonal horizontal-movement period entries | int | per_group | |
| iBioEroder | Whether the group is a bioeroder (mapped to XML “isBioEroder”) | int | per_group | |
| isSupplemented | Whether the group is supplemented (imported feed/stocking) | int | per_group | |
| isExternal | Whether the group is an externally-driven population (optional column, only when external_populations flag is on) | int | per_group | |
| isLandActive | Whether the group is active on land (optional column, only when terrestrial_on flag is on) | int | per_group | |
| isLightEffected | Whether the group is affected by light pollution (optional column, only when flag_pollutant_impacts is on) | int | per_group | |
| isNoiseEffected | Whether the group is affected by noise pollution (optional column, only when flag_pollutant_impacts is on) | int | per_group |
Physics
physics.prm
| Name | Description | Units | Type | Dimension |
|---|---|---|---|---|
| include_atmosphere | Switch enabling the atmospheric exchange concentrations block | int | scalar | |
| atmospheric_NH | Atmospheric ammonia concentration | mg N m-3 | double | scalar |
| atmospheric_NO | Atmospheric nitrate concentration | mg N m-3 | double | scalar |
| atmospheric_F | Atmospheric detritus/flux concentration | mg N m-3 | double | scalar |
| atmospheric_O2 | Atmospheric oxygen concentration | mg O m-3 | double | scalar |
| atmospheric_CO2 | Atmospheric carbon dioxide concentration | mg C m-3 | double | scalar |
| atmospheric_P | Atmospheric phosphorus concentration | mg P m-3 | double | scalar |
| atmospheric_Si | Atmospheric silica concentration | mg Si m-3 | double | scalar |
| mix_deep_O2 | Switch to include oxygen in deep-ocean remixing of bottom values | int | scalar | |
| vdiffwt_wc | Vertical diffusion weighting coefficient in the water column | double | scalar | |
| vdiffwt_sed | Vertical diffusion weighting coefficient in the sediment | double | scalar | |
| wc_kz | Water-column vertical diffusion (eddy diffusivity) coefficient | m2 s-1 | double | scalar |
| wc_dz_tol | Tolerance for water-column layer dz before reset to nominal value | fraction | double | scalar |
| maxseddz | Maximum sediment layer thickness | m | double | scalar |
| minseddz | Minimum sediment layer thickness | m | double | scalar |
| max_erosion | Maximum sediment erosion rate | m s-1 | double | scalar |
| wgt_georugosity | Weighting of geological rugosity in aragonite/rugosity tracking | double | scalar | |
| bi_dissol_kz | Bio-irrigation dissolved-tracer diffusion rate | m2 s-1 | double | scalar |
| bi_exchange | Bio-irrigation exchange rate | s-1 | double | scalar |
| bi_injection | Bio-irrigation injection rate | s-1 | double | scalar |
| bt_partic_kz | Bio-turbation particulate-tracer diffusion rate | m2 s-1 | double | scalar |
| bt_exchange | Bio-turbation exchange rate | s-1 | double | scalar |
| bt_expulsion | Bio-turbation expulsion rate | s-1 | double | scalar |
| biosedprofile | Functional form of depth dependence for bio-irrigation/turbation (first char used) | string | scalar | |
| biooxprofile | Functional form of depth dependence for sediment oxygen distribution (first char used) | string | scalar | |
| baseline_temp | Baseline temperature for the model | degrees C | double | scalar |
| temp_ampltiude | Amplitude of temperature variation (note key is misspelled in source) | degrees C | double | scalar |
| constrain_wc | Switch to constrain water depth to a minimum value of 1m | int | scalar | |
| mix_injection | Vertical upwelling mixing rate | s-1 | double | scalar |
| mix_season_kz | Seasonal vertical upwelling mixing coefficient | double | scalar | |
| mix_deep | Switch indicating whether deep ocean mixing occurs | int | scalar | |
| mix_deep_depth | Depth threshold for deep ocean mixing | m | double | scalar |
| injection | Switch to use point source/sink injection | int | scalar | |
| atmospherics | Switch to use atmospheric exchange model | int | scalar | |
| settling | Switch to use settling model | int | scalar | |
| bioirrigation | Switch to use bio-irrigation model | int | scalar | |
| bioturbation | Switch to use bio-turbation model | int | scalar | |
| horiz_diffusion | Switch to use horizontal diffusion model | int | scalar | |
| vert_diffusion | Switch to use vertical diffusion model | int | scalar | |
| vert_mix | Switch to use forced vertical mixing model | int | scalar | |
| advect_diffusion | Switch to use transport (advection-diffusion) model | int | scalar | |
| fill_zero_exchange | Switch to fill zero-exchange flows | int | scalar | |
| use_fill_horizmix | Switch to use horizontal mixing when filling zero exchanges | int | scalar | |
| flush_threshold | Flushing threshold triggering zero-exchange fill | double | scalar | |
| resuspension | Switch to use resuspension model | int | scalar | |
| decay_wc | Switch to use decay model in the water column | int | scalar | |
| decay_sed | Switch to use decay model in the sediment | int | scalar | |
| decay_sed_scale | Scalar for decay rate in the sediment | double | scalar | |
| scale_transport | Switch to scale exchanges/transport | int | scalar | |
| prcnt_exchange | Coefficient for constant scaling of exchanges | fraction | double | scalar |
| ka_exchange | Coefficient for area-corrected scaling of exchanges | double | scalar | |
| cascade_flows | Switch allowing flows/exchanges to cascade down slopes | int | scalar | |
| edge_type | Per-box boundary type flag (standard, absorptive or reflective); read into local bnd_type then stored as box edge_type | double_array | per_box | |
| eddy_S1 | Seasonal eddy scaling factor for season 1 (per box) | double_array | per_box | |
| eddy_S2 | Seasonal eddy scaling factor for season 2 (per box) | double_array | per_box | |
| eddy_S3 | Seasonal eddy scaling factor for season 3 (per box) | double_array | per_box | |
| eddy_S4 | Seasonal eddy scaling factor for season 4 (per box) | double_array | per_box | |
| eddy_mixscale | Coefficient for scaling of vertical exchanges by eddies | double | scalar | |
| nutrientchange | Number of gradual nutrient (point source/sink) changes to apply | int | scalar | |
| pulsechange | Switch/number for pulsed point source/sink changes | int | scalar | |
| pss<s>_numchanges | Number of point source/sink change schedules for point source s | int | per_group | |
| pss<s>_change<i> | Per-timestep flags marking which point sources are scaled in change i of source s | int_array | timeseries | |
| pss<s>_mult<i> | Per-timestep multipliers applied in change i of source s | double_array | timeseries | |
| pss<s>_period<i> | Per-timestep period over which change i of source s is applied | int_array | timeseries | |
| pss<s>_start<i> | Per-timestep start time for change i of source s | int_array | timeseries | |
| maxicedz | Maximum ice layer thickness | m | int | scalar |
| minicedz | Minimum ice layer thickness | m | int | scalar |
| num_ice_classes | Number of ice classes/types | int | scalar | |
| slush | Tracer/id index for slush ice | int | scalar | |
| kind_ice_model | Selector for which ice model formulation to use | int | scalar |
forcing_prm
| Name | Description | Units | Type | Dimension |
|---|---|---|---|---|
| use_pollutantfiles | Flag to enable noise/light pollution forcing tracer files | int | scalar | |
| use_phFiles | Flag to enable pH forcing files | int | scalar | |
| use_tempfiles | Flag to enable temperature forcing files | int | scalar | |
| use_saltfiles | Flag to enable salinity forcing files | int | scalar | |
| use_VertMixFiles | Flag to enable vertical mixing scalar forcing files | int | scalar | |
| n<shortName>files | Number of physical-property forcing files for a given property (temp/salt/pH/Wind/vertMixScalar/noise_pollution/light_pollution) | int | scalar | |
| <shortName>_rewind | Rewind flag for a physical-property forcing series | int | scalar | |
| <longName><i>.name | File name (i-th) of a physical-property forcing series (Temperature/Salinity/pH/Wind/vertMixScalar/Noise_Pollution/Light_Pollution) | string | other | |
| use_force_tracers | Flag to enable generic forcing-tracer (netCDF) input | int | scalar | |
| nforceTracers | Number of forcing tracers | int | scalar | |
| tracerNames | List of forcing-tracer variable names | string_array | other | |
| use_weighted_assim | Flag to use per-tracer assimilation weighting coefficients | int | scalar | |
| <tracerName>_nFiles | Number of forcing files for a given forcing tracer | int | scalar | |
| <tracerName>_File<i>.name | File name (i-th) for a given forcing tracer | string | other | |
| <tracerName>_File<i>.use_resets | Whether file i of a forcing tracer applies reset values | int | scalar | |
| <tracerName>_rewind | Rewind flag for a forcing tracer | int | scalar | |
| <tracerName>_wgt_coefft | Assimilation weighting coefficient for a forcing tracer | double | scalar | |
| <tracerName>_ResetTol | Reset tolerance for a forcing tracer | double | scalar | |
| use_move_entries | Flag to enable forced-movement distribution forcing | int | scalar | |
| nforceMoveGroups | Number of functional-group stages with forced movement distributions | int | scalar | |
| MoveGroupCodes | List of moving group/stage codes (e.g. <code>stage<n>) | string_array | other | |
| <moveGroupCode>_File.name | NetCDF distribution file for a moving group/stage | string | other | |
| <moveGroupCode>_tstart | Start time for applying forced movement of a group/stage | double | scalar | |
| Solar_radiation | Solar radiation forcing input filename (.ts or .nc); empty means Atlantis computes light | string | other | |
| <shortName>_rewind | Rewind flag for the solar-radiation (.nc) forcing series; shortName is “swr” | int | scalar | |
| Solar_radiation_rewind | Alternate rewind flag for the solar-radiation (.nc) forcing series | int | scalar | |
| nhdfiles | Number of hydrodynamic input (netCDF) files | int | scalar | |
| ts_on_hydro_time | Whether time series use the hydrodynamic time reference instead of model time | int | scalar | |
| inputs_tout | Output frequency for inputs.ts / export.ts files | seconds | double | scalar |
| hd<i>.name | File name (i-th) of a hydrodynamic input file | string | other | |
| nIcets | Number of ice time series (ts-file ice input); tsname is “Ice” | int | scalar | |
| typeIcets | Type of ice time series | int | scalar | |
| Icets<i>.data | Ice state time-series data filename for series i | string | other | |
| Icets<i>.depth_data | Ice depth time-series data filename for series i | string | other | |
| nInceFiles | Number of ice input netCDF files | int | scalar | |
| Ice<i>.name | File name (i-th) of an ice input netCDF file | string | other | |
| Precipitation | Precipitation time-series filename | mm day-1 | string | other |
| Evaporation | Evaporation time-series filename | mm day-1 | string | other |
| Tracer_area_inputs | Area tracer-input time-series filename | string | other | |
| thermal_index | Thermal-index lake-fish recruitment forcing time-series filename | deg C | string | other |
| thermal_index_rewind | Rewind flag for the thermal_index time series | int | scalar | |
| rate_index | Rate-index lake-fish recruitment forcing time-series filename | deg C | string | other |
| rate_index_rewind | Rewind flag for the rate_index time series | int | scalar | |
| Recruitment_time_series | Recruitment forcing time-series filename | string | other | |
| Recruitment_enviro_forcing | Recruitment environmental forcing time-series filename | string | other | |
| KWSR_forcing | KWSR environmental forcing time-series filename | string | other | |
| LinearMort | Linear-mortality scaling forcing time-series filename | string | other | |
| SizeChange | Size (sn/rn) change scaling forcing time-series filename | string | other | |
| GrowthRateChange | Growth-rate change forcing time-series filename | string | other | |
| FSPBChange | FSPB change forcing time-series filename | string | other | |
| pCO2_forcing | Atmospheric pCO2 forcing time-series filename | string | other | |
| use_external_scaling | Flag to enable external biology scalar (netCDF) forcing | int | scalar | |
| externalBiologyForcingFile | External biology scalar forcing netCDF filename | string | other | |
| externalBiologyForcingFile_rewind | Rewind flag for the external biology scalar forcing file | int | scalar | |
| scale_all_mortality | Whether external scaling applies to all mortality terms | int | scalar | |
| mortality_addition | Whether external mortality scaling is additive vs multiplicative | int | scalar | |
| use_larvalfiles | Flag to enable larval-dispersal connectivity matrix forcing | int | scalar | |
| larval_rewind | Rewind flag for the larval connectivity forcing file | int | scalar | |
| Larval0.name | Larval connectivity matrix netCDF filename | string | other |
Harvest
fisheries.csv
| Name | Description | Units | Type | File | Dimension |
|---|---|---|---|---|---|
| Code | Fishery code identifier | string | fisheries_csv | per_fishery | |
| Index | Fishery index number | int | fisheries_csv | per_fishery | |
| Name | Descriptive fishery name | string | fisheries_csv | per_fishery | |
| IsRec | Whether the fishery is recreational (1) or commercial (0) | int | fisheries_csv | per_fishery | |
| NumSubFleets | Number of subfleets in the fishery (also sets K_max_num_subfleet) | double | fisheries_csv | per_fishery |
harvest.prm
| Name | Description | Units | Type | File | Dimension |
|---|---|---|---|---|---|
| flag<f>day | Fishery active flag / day-night preference (2=no pref,1=day,0=night) | int | harvest_prm | per_fishery | |
| <f>_tStart | Day fishery starts operating | day | double | harvest_prm | per_fishery |
| <f>_tEnd | Day fishery stops operating | day | double | harvest_prm | per_fishery |
| <f>_start_manage | Day management of fishery starts | day | double | harvest_prm | per_fishery |
| <f>_end_manage | Day management of fishery ends | day | double | harvest_prm | per_fishery |
| flagfish<GRP> | Per-group fishing/targetting on-off flag | int | harvest_prm | per_group | |
| flaghabitat_<GRP> | Group habitat-association flag (impacted groups) | int | harvest_prm | per_group | |
| <f>_flagdempelfishery | Flag: demersal vs pelagic fishery | int | harvest_prm | per_fishery | |
| <f>_effortmodel | Effort-model option flag for fishery | int | harvest_prm | per_fishery | |
| dynanyway | Force dynamic catch evaluation even when not strictly needed | int | harvest_prm | scalar | |
| <f>_explore | Flag exploratory fishing has been done | int | harvest_prm | per_fishery | |
| <f>_effortdrop | Flag effort drop allowed | int | harvest_prm | per_fishery | |
| <f>_selcurve | Selectivity curve type for fishery | int | harvest_prm | per_fishery | |
| flagdiscard_<GRP> | Group discarding flag | int | harvest_prm | per_group | |
| flagescapement_<GRP> | Group escapement (gear-escape) flag | int | harvest_prm | per_group | |
| spawn_closure_<GRP> | Group spawning-closure flag | int | harvest_prm | per_group | |
| flag_access_thru_wc_<GRP> | Group accessible to gear through water column flag | int | harvest_prm | per_group | |
| flagimposecatch_<GRP> | Group uses imposed (forced) catch time series | int | harvest_prm | per_group | |
| flagF_<GRP> | Group uses imposed fishing-mortality (F) time series | int | harvest_prm | per_group | |
| flagchangediscrd | Global flag - discarding practices change with time | int | harvest_prm | scalar | |
| flagchangesel | Global flag - selectivity changes with time | int | harvest_prm | scalar | |
| flagchangeF | Global flag - F-mortality forcing changes with time | int | harvest_prm | scalar | |
| flagchangeq | Global flag - catchability changes with time | int | harvest_prm | scalar | |
| flagchangep | Global flag - spatial coverage changes with time | int | harvest_prm | scalar | |
| flagchangeswept | Global flag - gear swept-area changes with time | int | harvest_prm | scalar | |
| <f>_changeSEL | Per-fishery selectivity-change flag | int | harvest_prm | per_fishery | |
| <f>_changeP | Per-fishery spatial-coverage change flag | int | harvest_prm | per_fishery | |
| <f>_changeSWEPT | Per-fishery swept-area change flag | int | harvest_prm | per_fishery | |
| flagQchange_<GRP> | Group catchability-change flag | int | harvest_prm | per_group | |
| flagFchange_<GRP> | Group F-mortality-change flag | int | harvest_prm | per_group | |
| flagchangeDISCRD_<GRP> | Group discarding-change flag | int | harvest_prm | per_group | |
| k_mismatch | Reduction in gear effectiveness due to water-column mismatch | double | harvest_prm | scalar | |
| FisheryTargetSpecies<f> | Per-fishery binary vector of target functional groups | int_array | harvest_prm | per_fishery | |
| CatchAgeDistributions_<GRP> | Catch age-class distribution per impacted age-structured group | proportion | double_array | harvest_prm | per_group |
| highgrade_thresh | Catch-proportion threshold defining preferred (high-graded) cohort | proportion | double | harvest_prm | scalar |
| q_<GRP> | Per-group catchability across fisheries | double_array | harvest_prm | per_group | |
| qStock_<GRP>_<coh> | Stock-distribution of catchability per group/cohort/stock | double_array | harvest_prm | per_group | |
| Speed_boat | Speed of average commercial fishing vessel (converted to m/s) | m/hr (input; stored /3600 as m/s) | double | harvest_prm | scalar |
| Speed_recboat | Speed of average recreational vessel (converted to m/s) | m/hr (input; stored /3600 as m/s) | double | harvest_prm | scalar |
| KDEP_fishery | Sediment penetration depth of fishing gear | m | double | harvest_prm | scalar |
| FisheryHabitats<f> | Per-fishery habitat (cover-type) association vector | double_array | harvest_prm | per_fishery | |
| <f>_maxdepth | Maximum sea-floor depth fishery operates at | m | double | harvest_prm | per_fishery |
| <f>_mindepth | Minimum sea-floor depth fishery operates at | m | double | harvest_prm | per_fishery |
| k_pattern | Habitat patchiness pattern parameter for trawl mortality (must be > -1) | double | harvest_prm | scalar | |
| k_patches | Number of habitat patches for trawl-mortality patchiness | double | harvest_prm | scalar | |
| BoxHabitatProportion<f> | Per-fishery proportion of each box covered by associated habitat | proportion | double_array | harvest_prm | per_box |
| imposecatchstart_<GRP> | Group day imposed catch/F begins | day | int | harvest_prm | per_group |
| imposecatchend_<GRP> | Group day imposed catch/F ends | day | int | harvest_prm | per_group |
| reportscale_<GRP> | Catch-reporting scaling factor per group | double | harvest_prm | per_group | |
| mFC_<GRP> | Forced fishing mortality (F) per group across fisheries | 1/day (rate) | double_array | harvest_prm | per_group |
| <GRP>_mFC_startage | First age class subject to forced fishing mortality | int_array | harvest_prm | per_group | |
| <GRP>_mFC_endage | Last age class subject to forced fishing mortality | int_array | harvest_prm | per_group | |
| sel_<GRP> | Constant selectivity of group (biomass groups) per fishery | proportion | double_array | harvest_prm | per_group |
| sel_<GRP><coh> | Constant selectivity per age class of age-structured group per fishery | proportion | double_array | harvest_prm | per_group |
| <f>sel_b | Logistic selectivity curve slope parameter B | double | harvest_prm | per_fishery | |
| <f>sel_lsm | Logistic selectivity curve inflection point (length at 50%) | cm | double | harvest_prm | per_fishery |
| <f>sel_normsigma | Normal selectivity curve spread (sigma) | double | harvest_prm | per_fishery | |
| <f>sel_normlsm | Normal selectivity curve modal length | cm | double | harvest_prm | per_fishery |
| <f>sel_lognormsigma | Lognormal selectivity curve spread (sigma) | double | harvest_prm | per_fishery | |
| <f>sel_lognormlsm | Lognormal selectivity curve modal length | cm | double | harvest_prm | per_fishery |
| <f>sel_gammasigma | Gamma selectivity curve spread (sigma) | double | harvest_prm | per_fishery | |
| <f>sel_gammalsm | Gamma selectivity curve modal length | cm | double | harvest_prm | per_fishery |
| <f>sel_bisigma | Bimodal selectivity curve first spread (sigma) | double | harvest_prm | per_fishery | |
| <f>sel_bisigma2 | Bimodal selectivity curve second spread (sigma) | double | harvest_prm | per_fishery | |
| <f>sel_ampli | Bimodal selectivity curve amplitude | double | harvest_prm | per_fishery | |
| <f>sel_bilsm1 | Bimodal selectivity curve left modal length | cm | double | harvest_prm | per_fishery |
| <f>sel_bilsm2 | Bimodal selectivity curve right modal length | cm | double | harvest_prm | per_fishery |
| p_escape_<GRP> | Proportion of group escaping gear | proportion | double | harvest_prm | per_group |
| Ka_escape_<GRP> | Escapement curve coefficient Ka for group | double | harvest_prm | per_group | |
| Kb_escape_<GRP> | Escapement curve exponent Kb for group | double | harvest_prm | per_group | |
| prop_within | Proportion of quota above which high grading begins | proportion | double | harvest_prm | scalar |
| salethresh | Proportion of max market value below which market-based discarding begins | proportion | double | harvest_prm | scalar |
| <f>_maxsaleprice | Maximum sale price for fishery (market-based discarding) | double | harvest_prm | per_fishery | |
| DiscardAgeDistributions_<GRP> | Discard age-class distribution per impacted age-structured group | proportion | double_array | harvest_prm | per_group |
| ProportionDiscarding_<GRP> | Proportion of co-catch discarded per impacted group (over groups) | proportion | double_array | harvest_prm | per_group |
| FFCDR_<GRP> | Fixed proportion of fished cohort discarded per group (case selector) | proportion | double | harvest_prm | per_group |
| FC_case<GRP> | Age-dependant discarding case flag per group (selects A vs B curve) | int | harvest_prm | per_group | |
| FFCDR_<GRP>chrt | Per-age-class fixed discard proportion, case A (FC_case==0) | proportion | double_array | harvest_prm | per_group |
| FFCDR_<GRP>chrtB | Per-age-class fixed discard proportion, case B (FC_case==1) | proportion | double_array | harvest_prm | per_group |
| FCthreshli_<GRP> | Size (length) threshold below which group discarded | cm | double_array | harvest_prm | per_group |
| incidmort_<GRP> | Incidental (discard) mortality proportion per group | proportion | double | harvest_prm | per_group |
| k_retain_<GRP> | Proportion retained (size-based discarding) per group | proportion | double_array | harvest_prm | per_group |
| k_waste_<GRP> | Proportion discarded as waste (size-based discarding) per group | proportion | double_array | harvest_prm | per_group |
| <f>_sweptarea | Gear swept area per fishery | m2 | double | harvest_prm | per_fishery |
| <f>_sel_changes | Number of selectivity changes scheduled for fishery | int | harvest_prm | per_fishery | |
| Start<f> | Start day(s) of each selectivity change (Selectivity_Change) | day | double_array | harvest_prm | per_fishery |
| NewCurve<f> | New selectivity curve type at each selectivity change | double_array | harvest_prm | per_fishery | |
| ConstantValueAddition<f> | Additive constant to selectivity LSM at each change | double_array | harvest_prm | per_fishery | |
| SigmaValueAddition<f> | Additive constant to selectivity sigma at each change | double_array | harvest_prm | per_fishery | |
| <f>_p_changes | Number of spatial-coverage changes for fishery | int | harvest_prm | per_fishery | |
| Pchange<f> | Coverage-change values (day + new P) per fishery | double_array | harvest_prm | per_fishery | |
| <f>_swept_changes | Number of swept-area changes for fishery | int | harvest_prm | per_fishery | |
| SWEPTchange<f> | Swept-area-change values (day + new swept area) per fishery | double_array | harvest_prm | per_fishery | |
| <GRP>_discard_changes | Number of discarding changes per group | int | harvest_prm | per_group | |
| Start<GRP> | Start day of each discard change (Discard_Changes) | day | int_array | harvest_prm | per_group |
| ChangeThreshMult<GRP> | Multiplier applied to discard size threshold at each change | double_array | harvest_prm | per_group | |
| RetainMult<GRP> | Multiplier applied to retained proportion at each change | double_array | harvest_prm | per_group | |
| DiscardMult<GRP> | Multiplier applied to discard proportion at each change | double_array | harvest_prm | per_group | |
| WasteMult<GRP> | Multiplier applied to waste proportion at each change | double_array | harvest_prm | per_group | |
| <GRP>_q_changes | Number of catchability changes per group | int | harvest_prm | per_group | |
| Qchange<GRP> | Catchability-change values (day + new q) per fished group/fishery | double_array | harvest_prm | per_group | |
| <GRP>_mFC_changes | Number of fishing-mortality changes per group | int | harvest_prm | per_group | |
| mFCchange<GRP> | Fishing-mortality-change values (day + new mFC) per fished group/fishery | double_array | harvest_prm | per_group | |
| <GRP>_age_harvest | Age at which aquaculture group is harvested | int | harvest_prm | per_group |
Run parameters (run.prm)
| Name | Description | Units | Type | File | Dimension |
|---|---|---|---|---|---|
| ecotest | Ecology test/diagnostic verbosity flag | int | biology_prm | scalar | |
| availflag | Switch controlling how prey availability is interpreted | int | biology_prm | scalar | |
| flagrandom | Enable stochastic/random processes | int | biology_prm | scalar | |
| readin_popratio | Read population ratio (stock) data flag | int | biology_prm | scalar | |
| flagresp | Respiration submodel flag | int | biology_prm | scalar | |
| flagavgmig | Average migration flag | int | biology_prm | scalar | |
| flagbactstim | Bacterial stimulation flag | int | biology_prm | scalar | |
| flagtrackpops | Track populations flag | int | biology_prm | scalar | |
| flagseason | Seasonal forcing flag | int | biology_prm | scalar | |
| flaglight | Light limitation model flag | int | biology_prm | scalar | |
| flaglightopt | Light optimisation option | int | biology_prm | scalar | |
| lim_sun_hours | Limit primary production to daylight hours flag | int | biology_prm | scalar | |
| flagmodeltemp | Temperature dependence model flag | int | biology_prm | scalar | |
| flagq10 | Global Q10 temperature scaling flag | int | biology_prm | scalar | |
| O2case | Oxygen limitation case selector | int | biology_prm | scalar | |
| flagnut | Nutrient limitation flag | int | biology_prm | scalar | |
| flagmicro | Microbial loop flag | int | biology_prm | scalar | |
| flagtempchange | Apply prescribed temperature change flag | int | biology_prm | scalar | |
| flagsaltchange | Apply prescribed salinity change flag | int | biology_prm | scalar | |
| flagpHchange | Apply prescribed pH change flag | int | biology_prm | scalar | |
| flagstarve | Starvation mortality flag | int | biology_prm | scalar | |
| flagdegrade | Detritus degradation flag | int | biology_prm | scalar | |
| flagroc | Rate-of-change effects flag | int | biology_prm | scalar | |
| flaghomog_sp | Homogeneous spatial distribution flag | int | biology_prm | scalar | |
| flagagestruct | Age structure global flag | int | biology_prm | scalar | |
| flagsenesce | Senescence mortality flag | int | biology_prm | scalar | |
| flagtsforcerecruit | Time-series forced recruitment flag | int | biology_prm | scalar | |
| flag_modify_KWSR | Modify weight-at-spawn ratio flag | int | biology_prm | scalar | |
| flag_extpop_growth_option | External population growth option | int | biology_prm | scalar | |
| juv_transition_thresh | Juvenile-to-adult size transition threshold | double | biology_prm | scalar | |
| mat_transition_thresh | Maturity transition threshold | double | biology_prm | scalar | |
| norm_larval_distrib | Normalise larval distribution flag | int | biology_prm | scalar | |
| larvae_connect_only | Larvae connectivity-only flag | int | biology_prm | scalar | |
| enviro_independ_larvae | Environment-independent larvae flag | int | biology_prm | scalar | |
| flag_recruit_effect | Recruitment environmental effect flag | int | biology_prm | scalar | |
| flag_macro_model | Macrophyte/seagrass model flag | int | biology_prm | scalar | |
| flag_benthos_sediment_link | Benthos-sediment coupling flag | int | biology_prm | scalar | |
| flag_competing_epiff | Competing epibenthic filter feeders flag | int | biology_prm | scalar | |
| max_available_habitat | Maximum available habitat fraction | double | biology_prm | scalar | |
| flag_invert_biohab | Invertebrate biogenic habitat flag | int | biology_prm | scalar | |
| flag_olddiet | Use legacy diet handling flag | int | biology_prm | scalar | |
| flag_fine_ontogenetic_diets | Fine-grained per-age diet matrices flag | int | biology_prm | scalar | |
| UseHardFeedingWindow | Use hard (step) feeding window flag | int | biology_prm | scalar | |
| UseBiLogisticFeedingWindow | Use bi-logistic feeding window flag | int | biology_prm | scalar | |
| flag_satiation | Predator satiation flag | int | biology_prm | scalar | |
| flag_shrinkfat | Allow shrinking/fat loss flag | int | biology_prm | scalar | |
| flag_predratiodepend | Ratio-dependent predation flag | int | biology_prm | scalar | |
| flag_dynamicXRS | Dynamic reserve/structural ratio flag | int | biology_prm | scalar | |
| flag_repcostSpawn | Reproduction cost at spawning flag | int | biology_prm | scalar | |
| flag_lengthSN | Length from structural N flag | int | biology_prm | scalar | |
| XRS_cap | Cap on reserve-to-structural ratio | double | biology_prm | scalar | |
| flag_rel_cover | Relative cover model flag | int | biology_prm | scalar | |
| flag_report_water_detritus | Report water-column detritus flag | int | biology_prm | scalar | |
| flag_refuge_model | Prey refuge model flag | int | biology_prm | scalar | |
| flag_rugosity_model | Rugosity model flag | int | biology_prm | scalar | |
| flag_georugosity | Geological (background) rugosity flag | int | biology_prm | scalar | |
| RugCover_Coefft | Rugosity-cover relationship coefficient | double | biology_prm | scalar | |
| RugCover_Const | Rugosity-cover relationship constant | double | biology_prm | scalar | |
| RugCover_Cap | Rugosity-cover relationship cap | double | biology_prm | scalar | |
| min_rugosity | Minimum rugosity | double | biology_prm | scalar | |
| max_rugosity | Maximum rugosity | double | biology_prm | scalar | |
| rugosity_const | Rugosity baseline constant | double | biology_prm | scalar | |
| rugosity_bozec_a | Bozec rugosity model coefficient a | double | biology_prm | scalar | |
| rugosity_bozec_b | Bozec rugosity model coefficient b | double | biology_prm | scalar | |
| rugosity_bozec_c | Bozec rugosity model coefficient c | double | biology_prm | scalar | |
| rugosity_bozec_d | Bozec rugosity model coefficient d | double | biology_prm | scalar | |
| flagmodelpH | pH dynamics model flag | int | biology_prm | scalar | |
| pH_sensitivity_model | pH sensitivity model selector | int | biology_prm | scalar | |
| flagPHmortcase | pH mortality case selector | int | biology_prm | scalar | |
| pH_surface_depth | Surface pH layer depth boundary | m | double | biology_prm | scalar |
| pH_mid_depth | Mid pH layer depth boundary | m | double | biology_prm | scalar |
| pH_surface_coefft_T | Surface pH regression coefficient on temperature | double | biology_prm | scalar | |
| pH_surface_coefft_S | Surface pH regression coefficient on salinity | double | biology_prm | scalar | |
| pH_surface_coefft_O | Surface pH regression coefficient on oxygen | double | biology_prm | scalar | |
| pH_surface_const | Surface pH regression constant | double | biology_prm | scalar | |
| pH_mid_coefft_T | Mid-layer pH regression coefficient on temperature | double | biology_prm | scalar | |
| pH_mid_coefft_S | Mid-layer pH regression coefficient on salinity | double | biology_prm | scalar | |
| pH_mid_coefft_O | Mid-layer pH regression coefficient on oxygen | double | biology_prm | scalar | |
| pH_mid_const | Mid-layer pH regression constant | double | biology_prm | scalar | |
| pH_deep_coefft_T | Deep-layer pH regression coefficient on temperature | double | biology_prm | scalar | |
| pH_deep_coefft_S | Deep-layer pH regression coefficient on salinity | double | biology_prm | scalar | |
| pH_deep_coefft_O | Deep-layer pH regression coefficient on oxygen | double | biology_prm | scalar | |
| pH_deep_const | Deep-layer pH regression constant | double | biology_prm | scalar | |
| flagmodelArag | Aragonite saturation model flag | int | biology_prm | scalar | |
| K_max_num_DHW | Max number of degree heating weeks records | int | biology_prm | scalar | |
| Karag_A | Aragonite regression coefficient A | double | biology_prm | scalar | |
| Karag_B | Aragonite regression coefficient B | double | biology_prm | scalar | |
| Karag_C | Aragonite regression coefficient C | double | biology_prm | scalar | |
| Karag_pH | Aragonite regression coefficient on pH | double | biology_prm | scalar | |
| Kca_const | Calcium constant for calcification | double | biology_prm | scalar | |
| K_Ks | Calcification saturation half-constant | double | biology_prm | scalar | |
| Ksmother_coefft | Smothering coefficient | double | biology_prm | scalar | |
| Ksmother_const | Smothering constant | double | biology_prm | scalar | |
| Pads_r_t0 | Phosphate adsorption rate at reference temp | double | biology_prm | scalar | |
| Pads_K | Phosphate adsorption half-saturation | double | biology_prm | scalar | |
| Pads_KO | Phosphate adsorption oxygen dependence | double | biology_prm | scalar | |
| r_immob_PIP_t0 | Particulate inorganic P immobilisation rate at reference temp | double | biology_prm | scalar | |
| Enviro_turb | Environmental turbidity switch | int | biology_prm | scalar | |
| K_TUR | Turbidity half-saturation | double | biology_prm | scalar | |
| K_TUR_DEP | Turbidity depth dependence | double | biology_prm | scalar | |
| K_MAX_TUR | Maximum turbidity | double | biology_prm | scalar | |
| K_IRR | Irradiance half-saturation | double | biology_prm | scalar | |
| K_MAX_IRR | Maximum irradiance | double | biology_prm | scalar | |
| K_MIN_IRR | Minimum irradiance | double | biology_prm | scalar | |
| r_DC_T15 | Labile detritus carbon breakdown rate at 15C | d-1 | double | biology_prm | scalar |
| r_DL_T15 | Labile detritus breakdown rate at 15C | d-1 | double | biology_prm | scalar |
| r_DR_T15 | Refractory detritus breakdown rate at 15C | d-1 | double | biology_prm | scalar |
| r_DON_T15 | Dissolved organic N breakdown rate at 15C | d-1 | double | biology_prm | scalar |
| r_DSi_T15 | Dissolved silica regeneration rate at 15C | d-1 | double | biology_prm | scalar |
| FDR_DC | Fraction of refractory detritus to DC | double | biology_prm | scalar | |
| FDR_DL | Fraction of refractory detritus to DL | double | biology_prm | scalar | |
| FDON_D | Fraction of detritus to DON | double | biology_prm | scalar | |
| R_0_T15 | Base remineralisation rate at 15C | d-1 | double | biology_prm | scalar |
| R_D_T15 | Detritus remineralisation rate at 15C | d-1 | double | biology_prm | scalar |
| Dmax | Maximum depth for remineralisation | m | double | biology_prm | scalar |
| K_nit_T15 | Nitrification rate at 15C | d-1 | double | biology_prm | scalar |
| K_conc | Nitrification concentration half-saturation | double | biology_prm | scalar | |
| p_NH_anad | Proportion NH from anaerobic decomposition | double | biology_prm | scalar | |
| X_ON | Oxygen-to-nitrogen Redfield ratio | double | biology_prm | scalar | |
| X_CN | Carbon-to-nitrogen Redfield ratio | double | biology_prm | scalar | |
| X_CHLN | Chlorophyll-to-nitrogen ratio | double | biology_prm | scalar | |
| X_SiN | Silica-to-nitrogen ratio | double | biology_prm | scalar | |
| X_FeN | Iron-to-nitrogen ratio | double | biology_prm | scalar | |
| k_wetdry | Wet/dry weight conversion factor | double | biology_prm | scalar | |
| k_w_cdepth | Light attenuation coefficient at critical depth | m-1 | double | biology_prm | scalar |
| k_w_depth | Light attenuation coefficient with depth | m-1 | double | biology_prm | scalar |
| k_w_deep | Deep-water light attenuation coefficient | m-1 | double | biology_prm | scalar |
| k_w_shallow | Shallow-water light attenuation coefficient | m-1 | double | biology_prm | scalar |
| k_PN | Light attenuation per unit particulate N | double | biology_prm | scalar | |
| k_DON | Light attenuation per unit DON | double | biology_prm | scalar | |
| k_DL | Light attenuation per unit labile detritus | double | biology_prm | scalar | |
| k_IS | Light attenuation per unit inorganic suspended matter | double | biology_prm | scalar | |
| k_SED | Light attenuation per unit sediment | double | biology_prm | scalar | |
| KIOP_min | Minimum I-optimal half-saturation | double | biology_prm | scalar | |
| KIOP_shift | I-optimal shift parameter | double | biology_prm | scalar | |
| KI_avail | Irradiance availability scalar | double | biology_prm | scalar | |
| K_addepth | Additional depth offset for light calc | m | double | biology_prm | scalar |
| swr_scalar | Shortwave radiation scaling factor | double | biology_prm | scalar | |
| swr_const | Shortwave radiation constant | double | biology_prm | scalar | |
| swr_cos_coefft | Shortwave radiation seasonal cosine coefficient | double | biology_prm | scalar | |
| swr_cos_offset | Shortwave radiation seasonal cosine offset | double | biology_prm | scalar | |
| albedo_ice | Ice albedo | double | biology_prm | scalar | |
| k_bs | Light attenuation under bare snow | double | biology_prm | scalar | |
| k_bi | Light attenuation under bare ice | double | biology_prm | scalar | |
| k_rs | Light attenuation under refrozen snow | double | biology_prm | scalar | |
| k_ri | Light attenuation under refrozen ice | double | biology_prm | scalar | |
| R_bi | Reflectance of bare ice | double | biology_prm | scalar | |
| k_ice | Light attenuation coefficient for ice | m-1 | double | biology_prm | scalar |
| ka_star | Specific light absorption coefficient | double | biology_prm | scalar | |
| Tchange_max_num | Number of prescribed temperature-change records | int | biology_prm | scalar | |
| Tchange | Prescribed temperature-change time-series (value/time pairs) | degC | double_array | biology_prm | timeseries |
| Schange_max_num | Number of prescribed salinity-change records | int | biology_prm | scalar | |
| Schange | Prescribed salinity-change time-series | double_array | biology_prm | timeseries | |
| pHchange_max_num | Number of prescribed pH-change records | int | biology_prm | scalar | |
| PHchange | Prescribed pH-change time-series | double_array | biology_prm | timeseries | |
| RTOP | Top of refuge tolerance | double | biology_prm | scalar | |
| K_Lc | Critical light constant | double | biology_prm | scalar | |
| RelTol | Relative numerical tolerance | double | biology_prm | scalar | |
| Flux_tol | Flux tolerance threshold | double | biology_prm | scalar | |
| min_pool | Minimum tracer pool concentration | double | biology_prm | scalar | |
| min_dens | Minimum density threshold | double | biology_prm | scalar | |
| min_channel_depth | Minimum channel depth | m | double | biology_prm | scalar |
| flag_do_var_express | Variable expression flag (evolution) | int | biology_prm | scalar | |
| flag_do_evolution | Enable evolution module | int | biology_prm | scalar | |
| flag_bound_change | Allow trait bound change flag | int | biology_prm | scalar | |
| flag_inheritance | Trait inheritance flag | int | biology_prm | scalar | |
| flag_evolvar_capped | Cap evolved variance flag | int | biology_prm | scalar | |
| evol_stdev_range | Evolutionary standard deviation range | double | biology_prm | scalar | |
| max_rate_evol | Maximum rate of evolutionary change | double | biology_prm | scalar | |
| flag_mult_grow_curves | Multiple growth morph curves flag | int | biology_prm | scalar | |
| ActiveTrait/<GRP> | Per-group active evolutionary trait flags (one row of trait toggles per group) | double_array | biology_prm | per_group | |
| MB_wc | Microbial biomass water-column reference | double | biology_prm | scalar | |
| eddy_scale | Eddy diffusivity scaling for PP | double | biology_prm | scalar | |
| XPB_DL | Fraction of PB flux to labile detritus | double | biology_prm | scalar | |
| XBB_DL | Fraction of BB flux to labile detritus | double | biology_prm | scalar | |
| XPB_DR | Fraction of PB flux to refractory detritus | double | biology_prm | scalar | |
| XBB_DR | Fraction of BB flux to refractory detritus | double | biology_prm | scalar | |
| k_PB | Pelagic bacteria rate constant | double | biology_prm | scalar | |
| k_BB | Benthic bacteria rate constant | double | biology_prm | scalar | |
| flaghabdepend | Habitat-dependent processes flag | int | biology_prm | scalar | |
| flag_move_habdepend | Habitat-dependent movement flag | int | biology_prm | scalar | |
| flagenviro_displace | Environmental displacement flag | int | biology_prm | scalar | |
| flagenviro_kill | Environmental kill flag | int | biology_prm | scalar | |
| REEFchange_max_num | Number of reef-cover change records | int | biology_prm | scalar | |
| FLATchange_max_num | Number of flat-cover change records | int | biology_prm | scalar | |
| SOFTchange_max_num | Number of soft-cover change records | int | biology_prm | scalar | |
| REEFchange | Reef-substrate cover change time-series | double_array | biology_prm | timeseries | |
| FLATchange | Flat-substrate cover change time-series | double_array | biology_prm | timeseries | |
| SOFTchange | Soft-substrate cover change time-series | double_array | biology_prm | timeseries | |
| Group_Habitat_Preference/<GRP> | Per-group habitat preference array over habitat types | double_array | biology_prm | per_group | |
| Group_Ice_Preference/<GRP> | Per-group ice habitat preference array | double_array | biology_prm | per_group | |
| Group_IceReprod_Preference/<GRP> | Per-group ice reproduction preference array | double_array | biology_prm | per_group | |
| roc_wgt | Rate-of-change weighting | double | biology_prm | scalar | |
| k_roc_food | Rate-of-change food scaling constant | double | biology_prm | scalar | |
| flagtempdepend_move | Temperature-dependent movement flag | int | biology_prm | scalar | |
| flagtempdepend_reprod | Temperature-dependent reproduction flag | int | biology_prm | scalar | |
| flagsaltdepend | Salinity-dependent processes flag | int | biology_prm | scalar | |
| flagO2depend | Oxygen-dependent processes flag | int | biology_prm | scalar | |
| flagconstrain_epiwander | Constrain epibenthic wandering flag | int | biology_prm | scalar | |
| X_RS | Reserve-to-structural target ratio | double | biology_prm | scalar | |
| Kthresh1 | Movement/feeding threshold constant 1 (read twice; two threshold slots) | double | biology_prm | scalar | |
| KHTD | Habitat threshold constant (deep) | double | biology_prm | scalar | |
| KHTI | Habitat threshold constant (intertidal) | double | biology_prm | scalar | |
| SeasonalDistribution/<GRP>/<STAGE> | Per-group/per-stage seasonal horizontal distribution (juvenile/adult, per box) | double_array | biology_prm | per_box | |
| p_BBfish | Proportion bacteria cleaned from fish-ingested detritus | double | biology_prm | scalar | |
| p_BBben | Proportion bacteria cleaned from benthic-ingested detritus | double | biology_prm | scalar | |
| p_PBwc | Proportion of pelagic bacteria available in water column | double | biology_prm | scalar | |
| p_PBben | Proportion of pelagic bacteria available in benthos | double | biology_prm | scalar | |
| k_refDL | Reference labile-detritus level for omnivore supplement feeding | double | biology_prm | scalar | |
| k_refDR | Reference refractory-detritus level for supplement feeding | double | biology_prm | scalar | |
| k_refsDL | Reference sediment labile-detritus level | double | biology_prm | scalar | |
| flagfishrates | Use fish-specific clearance/growth rates flag | int | biology_prm | scalar | |
| li_a_invert | Length-weight allometry coefficient a for invertebrates | double | biology_prm | scalar | |
| li_b_invert | Length-weight allometry exponent b for invertebrates | double | biology_prm | scalar | |
| pPREY<PREDCOHORT><PRED><PREYCOHORT> | Vertebrate predator-prey availability matrix (pSPVERTeat), availability of each prey group to a predator age class | double_array | biology_prm | per_prey | |
| pPREY<PRED> | Invertebrate/biomass-pool predator-prey availability row (single cohort) | double_array | biology_prm | per_prey | |
| DetritusSedimentFoodAvail/<GRP>[/<COHORT>] | Availability of detritus/sediment groups to a predator (per detritus group, per cohort for age-structured) | double_array | biology_prm | per_prey | |
| AgeDietAvail/<GRP> | Fine ontogenetic (per-age) prey availability matrix | double_array | biology_prm | per_prey | |
| SeagrassFoodAvail/<GRP> | Availability of seagrass/macrophyte parts to grazers | double_array | biology_prm | per_prey | |
| Supplemental_Diets/<GRP> | Imported/supplemental feed distribution per box for cultured/supplemented groups | double_array | biology_prm | per_box | |
| Catch_Opportunity/Catch_Availability/<GRP> | Availability of fishery catch to opportunistic catch-eaters (per prey group) | double_array | biology_prm | per_prey | |
| Catch_Opportunity/Proportion_Exploitable/<GRP> | Proportion of each fishery’s catch exploitable by catch-eaters | double_array | biology_prm | other | |
| C_<GRP> | Per-cohort vertebrate clearance (search-volume) rate; prm key C_<GRP> array over age classes | m3 (mg N)-1 d-1 | double_array | biology_prm | per_cohort |
| C_<GRP>_T15 | Invertebrate grazer clearance rate at 15C; scalar per group | m3 (mg N)-1 d-1 | double | biology_prm | per_group |
| mum_<GRP> | Per-cohort vertebrate maximum growth (consumption) rate; prm key mum_<GRP> array over age classes | mg N d-1 (per individual) | double_array | biology_prm | per_cohort |
| mum_<GRP>_T15 | Invertebrate/PP/bacteria maximum growth rate at 15C; scalar per group | d-1 | double | biology_prm | per_group |
| InvertebrateSN/<GRP> | Invertebrate structural-N (size) reference per group | mg N | double_array | biology_prm | per_group |
| Q10 | Global Q10 temperature scaling factor | double | biology_prm | scalar | |
| temp_coefftB | Temperature response coefficient B | double | biology_prm | scalar | |
| temp_coefftC | Temperature response coefficient C | double | biology_prm | scalar | |
| temp_exp | Temperature response exponent | double | biology_prm | scalar | |
| KST_fish | Standard metabolic temperature scalar - fish | double | biology_prm | scalar | |
| KST_shark | Standard metabolic temperature scalar - shark | double | biology_prm | scalar | |
| KST_bird | Standard metabolic temperature scalar - bird | double | biology_prm | scalar | |
| KST_mammal | Standard metabolic temperature scalar - mammal | double | biology_prm | scalar | |
| Ktmp_fish | Temperature respiration coefficient - fish | double | biology_prm | scalar | |
| Ktmp_shark | Temperature respiration coefficient - shark | double | biology_prm | scalar | |
| Ktmp_bird | Temperature respiration coefficient - bird | double | biology_prm | scalar | |
| Ktmp_mammal | Temperature respiration coefficient - mammal | double | biology_prm | scalar | |
| Kthreshm | Mortality threshold constant | double | biology_prm | scalar | |
| FFDDR | Fraction of feeding-derived detritus going to refractory pool | double | biology_prm | scalar | |
| FDL_fish | Fraction labile detritus from fish mortality | double | biology_prm | scalar | |
| FDL_benth | Fraction labile detritus from benthic invert mortality | double | biology_prm | scalar | |
| FDL_top | Fraction labile detritus from top predator mortality | double | biology_prm | scalar | |
| FDL_wc | Fraction labile detritus from water-column group mortality | double | biology_prm | scalar | |
| FDL_SG_roots | Fraction labile detritus from seagrass roots | double | biology_prm | scalar | |
| FDL_SG_leaves | Fraction labile detritus from seagrass leaves | double | biology_prm | scalar | |
| FPB_DR | Fraction pelagic-bacteria flux to refractory detritus | double | biology_prm | scalar | |
| FBB_DR | Fraction benthic-bacteria flux to refractory detritus | double | biology_prm | scalar | |
| FPB_DON | Fraction pelagic-bacteria flux to DON | double | biology_prm | scalar | |
| FBB_DON | Fraction benthic-bacteria flux to DON | double | biology_prm | scalar | |
| Fben_den | Fraction benthic denitrification | double | biology_prm | scalar | |
| ImplicitSeabirdMortalityRate/<GRP> | Implicit (external) seabird mortality rate per group | d-1 | double_array | biology_prm | per_group |
| ImplicitFishMortalityRate/<GRP> | Implicit (external) fish mortality rate per group | d-1 | double_array | biology_prm | per_group |
| flagtrecruitdistrib | Time-varying recruit distribution flag | int | biology_prm | scalar | |
| recover_trigger | Population recovery trigger level | double | biology_prm | scalar | |
| recover_span | Recovery span duration | double | biology_prm | scalar | |
| recover_subseq | Subsequent recovery parameter | double | biology_prm | scalar | |
| lognorm_mu | Lognormal recruitment mean parameter | double | biology_prm | scalar | |
| lognorm_sigma | Lognormal recruitment standard deviation parameter | double | biology_prm | scalar | |
| rec_m | Recruitment mean (stochastic) parameter | double | biology_prm | scalar | |
| rec_sigma | Recruitment standard deviation parameter | double | biology_prm | scalar | |
| recruitRange | Recruitment search range | double | biology_prm | scalar | |
| recruitRangeFlat | Flat recruitment range | double | biology_prm | scalar | |
| ref_chl | Reference chlorophyll for recruitment effect | double | biology_prm | scalar | |
| FSPB_<GRP> | Per-cohort proportion of spawning biomass; prm key FSPB_<GRP> array over age classes | double_array | biology_prm | per_cohort | |
| KDENR_<GRP> | Per-cohort density-dependent recruitment parameter (Reproduction/KDENR) | double_array | biology_prm | per_cohort | |
| recSTOCK_<GRP> | Per-stock recruitment allocation (Reproduction/recSTOCK) | double_array | biology_prm | other | |
| popratioStock_<GRP> | Per-stock population ratio at initialisation (Reproduction/popratioStock) | double_array | biology_prm | other | |
| pStock_<GRP> | Per-stock diet/spatial proportion (Diet/pStock) | double_array | biology_prm | other | |
| VerticalRecruitLocation/<GRP> | Per-group vertical layer distribution for recruits | double_array | biology_prm | per_layer | |
| RecruitDistribution/<GRP> | Per-group horizontal recruit distribution over boxes | double_array | biology_prm | per_box | |
| AquacultDistribution/<GRP> | Per-group horizontal aquaculture stocking distribution over boxes | double_array | biology_prm | per_box | |
| <GRP>_Time_Spawn | Per-spawn-event spawning time-of-year per group (prm key *_Time_Spawn) | day-of-year | int_array | biology_prm | per_cohort |
| Time_Age_<GRP> | Per-event time-to-age cohort entry per group (prm key Time_Age_<GRP>) | day | int_array | biology_prm | per_cohort |
| StockStructure/<GRP> | Per-group per-box stock membership (integer stock id per box) | int_array | biology_prm | per_box | |
| VerticalStockStructure/<GRP> | Per-group per-layer vertical stock membership | int_array | biology_prm | per_layer | |
| invading_sp_model | Invading-species model flag | int | biology_prm | scalar | |
| InvaderIndex | Functional-group index of the invader | int | biology_prm | scalar | |
| minInvaderAge | Minimum age of invading individuals | int | biology_prm | scalar | |
| maxInvaderAge | Maximum age of invading individuals | int | biology_prm | scalar | |
| InvaderEntryBox | Box index where invader enters | int | biology_prm | scalar | |
| InvadersEntering | Number of invaders entering | double | biology_prm | scalar | |
| InvaderMinDepth | Minimum entry depth for invader | m | double | biology_prm | scalar |
| InvaderMaxDepth | Maximum entry depth for invader | m | double | biology_prm | scalar |
| InvaderStartDay | Day-of-year invasion starts | day-of-year | int | biology_prm | scalar |
| InvaderEndDay | Day-of-year invasion ends | day-of-year | int | biology_prm | scalar |
| InvaderScalar | Scaling of invader numbers | double | biology_prm | scalar | |
| InvaderSpeed | Invader movement speed | double | biology_prm | scalar | |
| InvaderEntryLayer | Vertical layer of invader entry | int | biology_prm | scalar | |
| p_IBice | Proportion of biota associated with ice | double | biology_prm | scalar | |
| flag_dissolved_pollutants | Track dissolved pollutants flag | int | biology_prm | scalar | |
| flag_contamMortModel | Contaminant mortality model flag | int | biology_prm | scalar | |
| flag_contamInteractModel | Contaminant interaction model flag | int | biology_prm | scalar | |
| flag_contamGrowthModel | Contaminant growth-effect model flag | int | biology_prm | scalar | |
| flag_contamReprodModel | Contaminant reproduction-effect model flag | int | biology_prm | scalar | |
| flag_contamOnlyAmplify | Contaminant amplify-only flag | int | biology_prm | scalar | |
| flag_contamMove | Contaminant movement flag | int | biology_prm | scalar | |
| flag_contamMinTemp | Contaminant minimum-temperature flag | int | biology_prm | scalar | |
| flag_contam_halflife_spbased | Species-based contaminant half-life flag | int | biology_prm | scalar | |
| flag_contamMaternalTransfer | Maternal contaminant transfer flag | int | biology_prm | scalar | |
| flag_contam_distrib | Contaminant distribution flag | int | biology_prm | scalar | |
| biopools_dodge_contam | Biological pools bypass contaminant flag | int | biology_prm | scalar | |
| min_pool_cont | Minimum contaminant pool concentration | double | biology_prm | scalar | |
| contam_tau | Contaminant decay time constant | double | biology_prm | scalar | |
| contam_sig_uptake_const | Contaminant sigmoidal uptake constant | double | biology_prm | scalar | |
| flag_detritus_contam | Detritus contaminant tracking flag | int | biology_prm | scalar | |
| k_migslow | Migration slowdown constant | double | biology_prm | scalar | |
| Migration/MigrateIOBox/<GRP>[/<COHORT>]/Migrate<N> | Per-migration destination box proportions for migrating groups | double_array | biology_prm | per_box | |
| Migration/KMIG_DEN/<GRP> | Initial density of pre-existing out-of-model migrators | double_array | biology_prm | per_cohort | |
| Migration/KMIG_RN/<GRP> | Initial reserve N of pre-existing out-of-model migrators | mg N | double_array | biology_prm | per_cohort |
| Migration/KMIG_SN/<GRP> | Initial structural N of pre-existing out-of-model migrators | mg N | double_array | biology_prm | per_cohort |
| Migration/KMIG_INVERT<N>/<GRP> | Initial density of out-of-model invertebrate migrators per migration | double_array | biology_prm | per_cohort | |
| flag<GRP> | Group functioning (on/off) flag | int | biology_prm | per_group | |
| flagdem<GRP> | Preferred-location (demersal) trend flag | int | biology_prm | per_group | |
| flagplankfish<GRP> | Planktivore flag | int | biology_prm | per_group | |
| <GRP>thresh | Flux threshold for sediment/bacteria flux | double | biology_prm | per_group | |
| <GRP>damp | Flux damping coefficient | double | biology_prm | per_group | |
| SPECIES_FAMILY Reproduction_flags | Per-group reproduction flags and parameters. One entry each, prm key = base_GRP: flagbearlive (live-bearing), feed_while_spawn, flagmother (parental care), flagrecruit (recruitment function id), flagrecpeak, flagstocking, flagkeep_plusgroup, Recruit_Period, Recruit_Time, cohort_recruit_entry, spawn_period, KSPA (spawn area), FSP (spawn fraction), Kcov_juv/Bcov_juv_/Acov_juv_/Kcov_ad_/Bcov_ad_/Acov_ad_ (cover coeffts), RugCover_scalar, age_mat (age at maturity), recover_start, KWSR, KWRR_, recover_mult_, BHbeta_/BHalpha_ (Beverton-Holt), Rbeta_/Ralpha_ (Ricker), PP_ (constant recruits), log_mult, norm_sigma, flag_recruit_stochastic, prod_alpha, den_depend_beta1/beta2, temp_coefft_, rate_coefft_, wind_coefft_, rec_var_, min/max_spawn_temp, min/max_spawn_salt, prop_spawn_lost, jack_a/jack_b_, rec_HabDepend, intersp_depend_recruit_/sp_/scale_, aquacult_fry, KA_/KB_ (weight-length). | varies | double | biology_prm | per_group |
| overwinterStartTofY_<GRP> | Overwinter start time-of-year (encystment block) | day-of-year | double | biology_prm | per_group |
| SPECIES_FAMILY Overwinter_Encystment | Per-group overwintering/encystment params: overwinterStartTofY_, overwinterEndTofY_, overwinterStartTemp_, overwinterEndTemp_, crit_mum_, crit_nut_, crit_temp_, encyst_rate_, hatch_rate_, encyst_period_, flagencyst_. | varies | double | biology_prm | per_group |
| SPECIES_FAMILY Evolution | Per-group evolution params: max_prop_shift_, inheritance_, trait_variance_, min_trait_variance_. | double | biology_prm | per_group | |
| SPECIES_FAMILY FeedingDetritusFractions | Per-group fractions of feeding-derived material to detritus: FDM_<GRP> (mortality detritus), FDG_<GRP> (egesta), FDGDL_, FDGDR_. | double | biology_prm | per_group | |
| SPECIES_FAMILY FeedingDynamics | Per-group/predator feeding parameters: catcheater, flagactiveDAY (diel activity), vla<GRP>T15 (assimilation), KL<GRP>/KU_<GRP>/KUP_<GRP>/KLP_<GRP> (feeding window lower/upper), Kmax_coefft_<GRP>, KDEP_<GRP> (sediment penetration depth), vlb_, hta_, htb_ (handling time), pR_ (reserve proportion fed), li_a_/li_b_/linf_/Kbert_/tzero_ (length-at-age, VB), min_li_mat_, predcase (functional response type), age_structured_prey_, p_split_, extra_feed, vl<GRP> (invert search volume), ht_ (invert handling time), hvm_, turbid_refuge_, RSmax_/RSmid_/RSslope_/RSprop_/SNcost_/RNcost_/RSstarve_ (reserve dynamics), E_<GRP>/EPlant_<GRP>/EDL_<GRP>/EDR_<GRP> (assimilation efficiencies on prey/plant/labile/refractory). | varies | double | biology_prm | per_group |
| SPECIES_FAMILY Q10_Temperature | Per-group temperature response: flagq10eff, flagq10receff, q10_<GRP>, q10_method_, q10_optimal_temp_, q10_correction_, temp_coefftA_, flagtempsensitive, flagfecundsensitive. | double | biology_prm | per_group | |
| SPECIES_FAMILY Salinity_pH_sensitivity | Per-group salinity/pH sensitivity: flagSaltSensitive, salt_correction_, flagpHsensitive, pHsensitive_model_, pH_constA_/B_/C_, min_pH_/max_pH_, KN_pH_, optimal_pH_, pH_correction_, contract_tol_, flagcontract_tol_, flagpredavaileffect, flagnutvaleffect, pHmortstart_, pHmortA_/B_, pHmortmid_. | double | biology_prm | per_group | |
| SPECIES_FAMILY Pollution_impact | Per-group pollution light/noise sensitivity coefficients: light_coefft_, noise_coefft_. | double | biology_prm | per_group | |
| SPECIES_FAMILY PrimaryProducer_uptake | Per-PP/seagrass parameters: KTUR_ (bioturbation), KIRR_ (infauna irradiance), KN_ (DIN half-sat), KS_ (Si half-sat), KF_ (Fe half-sat), flag*lim, KI_<GRP>T15 (light half-sat), L_KI<GRP>T15 (seagrass leaf light), Kext/Ksub_/KN_epi_/KsubEpi_/Ktrans_ (seagrass), Beta_D_, PBmax_D_, P_uptake_/P_scale_uptake_/P_concp_/P_min_internal_/P_max_internal_, C_uptake_/C_scale_uptake_/C_concp_, PSA_min_/C_min_, Phyto_Resp_Rate_, KP_ (P half-sat), KLYS_ (lysis rate), FSBDR_. | varies | double | biology_prm | per_group |
| SPECIES_FAMILY Mortality | Per-group/per-cohort mortality rates at 15C: mQ (quadratic), mL (linear), mLext (external linear), mPext (external proportional); plus mS<GRP>T15 (macrophyte senescence), mStarve (starvation), mT (temperature mortality), mD (depth-oxygen), mO (oxygen), KO2_ (lethal O2), KO2LIM_ (limiting O2), turbidity mortality _turbid_L/_turbid_a/_turbid_b. The _mQ/_mL/_mLext/_mPext and turbidity entries are read per-cohort via Read_Cohort_Species_Param_Values; others via Util_XML_Read_Species_Param. | d-1 | double | biology_prm | per_cohort |
| SPECIES_FAMILY Physical_limits_movement | Per-group physical limitation and movement: low_/max_/sat_/thresh (basal/sed-FF feeding limits), _ddepend_move (movement model), _max/min_move_temp, _max/min_move_salt, _K_temp_const, K_salt_const, Speed, _mindepth/_maxdepth/_maxtotdepth, _min_O2, _K_o2_const, _homerangerad, _overlap, k_trans, _remin_contrib. | varies | double | biology_prm | per_group |
| SPECIES_FAMILY Coral_Sponge | Per-group coral/sponge params (bleaching, calcification, rugosity, smothering): _bleach_periodA/B, _mBleach, _bleaching_rate, _bleach_recovery_rate, _bleach_tempshift, _bleach_growshift, _bleach_temp, _min_bleach_temp, _prop_zooxanth, _DHW_thresh, _threshdepth, _depmum_scalar, _min/max_bleach_salt, _HostRemin, _calcifRefBaseline, _calcifTconst/Tcoefft/Topt/Lambda, _FeedLightThresh, _PropLightFeed, _coral_max_accel_trans/A/B, _CrecruitA/B/C, _coral_overgrow, _coral_compete, _sponge_overgrow, _sponge_compete, _Ksmother_A/B, _Vmax_deltaSi, _Km_deltaSi, _rug_erode, _rug_bleacherode, _rugFeedScalar, _rug_factor, _colony_ha, _rug_erode_sponge, _rugosity_inc/_rugosity_dec, _colony_diam. | varies | double | biology_prm | per_group |
| SPECIES_FAMILY Fishing_targetting | Per-group fishing/management flags read from bio prm: flagfish (targeting), flag_access_thru_wc_, age_harvest (aquaculture), tier (HCR tier), regionalSP, basketSP, basket_size, max_co_sp, coType_, tac_resetperiod, cpue_cdf_poor_r_/p_, cpue_cdf_top_r_/p_, samplesize, allometic li_a/li_b/li_bin/li_start/li_max, R_max, avg_inv_size, flag_assess, assess_bootstrap, assess_nat_mort, flag_prod_model, top_pcnt, bot_pcnt, assess_datastream, whichRAssess_, ICE_KDEP_. | varies | double | biology_prm | per_group |
| SPECIES_FAMILY RBC_assessment | Per-group reference-biomass-control / stock-assessment parameters (RBCSpeciesParamStructArray, atUtilXML.c:511-636): DiscType_, MaxH_, Growthage_L1_/L2_, MinCatch_, AssessStart_, NumRegions_, Nsexes_, Tier1/2/3Sig_, isTriggerSpecies_, trigger_threshold_, UseRBCAveraging_, Maturity_Inflect_/Slope_, T1_steep_phase_, tiertype_, Tier3_* (Fcalc/time/maxage/M/S25/S50/F/h/matlen/maxF), CCsel_years_, Tier4_* (avtime/CPUEyrmin/max/m/alpha/Cmaxmult/Bo_correct), Tier5_* (length/S50/cv/flt/reg/p/sel/q), PostRule_, CPUEmult_, MaxChange_, TriggerResponseScen_, MG_offset_, Regime_shift_assess_, RecDevBack_, Hsteep_, Agesel_Pattern_, AssessFreq_, BallParkF_/Yr_, NumChangeLambda_, num_enviro_obs_, num_growth_morphs_, Nsex_samp_, MaxAge_, Nyfuture_, NumFisheries_, Nlen_, Lbin_, thresh_mat_, femsexratio_, flagLAdirect_/SLAdirect_/WAdirect_, SigmaR1_/R2_/R_future_, PSigmaR1_, Regime_year_, RecDevMinYr_/MaxYr_, RecDevFlag_, AutoCorRecDev_, LFSSlim_, AFSSlim_, NumSurvey_, Regime_year_assess_, NblockPattern_, SRBlock_, assRecDevMinYear_, MultispAssessType_, mgt_indicator_, init_mgt_category_/sp_, PGMSYBHalpha_/beta_. | varies | double | biology_prm | per_group |
Abbreviations
atl$abbreviation
#> $GRP
#> [1] "species (functional) group code, e.g. FPS; range 0..K_num_tot_sp-1"
#>
#> $f
#> [1] "fishery name/code (per-fishery harvest parameters, bm->FISHERYprms[f])"
#>
#> $id
#> [1] "species-parameter index into FunctGroupArray[guild].speciesParams[<id>] (slot in the speciesParamStructArray[] master table)"
#>
#> $base
#> [1] "parameter base-name prefix in per-group keys of the form <base>_<GRP> (e.g. mum, C); uppercase <BASE> used in comment blocks"
#>
#> $i
#> [1] "loop index: file index in a forcing-file series (e.g. hd<i>.name, <tracerName>_File<i>.name) or change-schedule index in pss keys (pss<s>_change<i>)"
#>
#> $s
#> [1] "point source/sink index, 0..npss-1 (e.g. pss<s>_numchanges)"
#>
#> $tracerName
#> [1] "name of a generic forcing tracer (netCDF forcing input, bm->forceTracerInput[])"
#>
#> $PRED
#> [1] "predator group code in diet-availability keys pPREY<PREDCOHORT><PRED><PREYCOHORT>"
#>
#> $N
#> [1] "migration event index (Migrate<N>: 1..num_migrate; KMIG_INVERT<N>: 0..num_migrate-1)"
#>
#> $shortName
#> [1] "short name of a physical-property forcing series (e.g. temp, salt, pH, Wind, vertMixScalar) used in keys like n<shortName>files"
#>
#> $COHORT
#> [1] "age class (cohort) of an age-structured group, e.g. in MigrateIOBox/<GRP>[/<COHORT>]/Migrate<N>"
#>
#> $suffix
#> [1] "parameter suffix in per-group keys of the form <GRP>_<suffix>; uppercase <SUFFIX> used in comment blocks"
#>
#> $moveGroupCode
#> [1] "moving group/stage code listed in MoveGroupCodes (forced-movement entries, form <code>_stage_<n>)"
#>
#> $coh
#> [1] "age-class (cohort) index in harvest keys, e.g. qStock_<GRP>_<coh>, sel_<GRP><coh>"
#>
#> $PREYCOHORT
#> [1] "prey life-stage digit in pPREY keys (1 = juvenile, 2 = adult)"
#>
#> $PREDCOHORT
#> [1] "predator life-stage digit in pPREY keys (1 = juvenile, 2 = adult)"
#>
#> $n
#> [1] "stage number in a moving group/stage code <code>_stage_<n>"
#>
#> $longName
#> [1] "long name of a physical-property forcing series (e.g. Temperature, Salinity) used in <longName><i>.name"
#>
#> $code
#> [1] "group code part of a moving group/stage code <code>_stage_<n>"
#>
#> $STAGE
#> [1] "life stage, juvenile or adult (e.g. SeasonalDistribution/<GRP>/<STAGE>)"