AtlantisGroupTypes
Group Types:
The type of the group determines many things, its habitat, the processes it carries out and what parameters are read in.
Vertebrate Groups
The vertebrate groups are:
FISH
BIRD
MAMMAL
SHARK
These should be set based on the old values in your biology.prm file isbird, ishark and ismammal. If the group is not a bird, shark or a mammal then it is assumed to be a fish.
Invertebrate Groups
The invertebrate group types are the following:
| Group Type | Description | Location | Large Groups - Processed Once per timestep |
|---|---|---|---|
| LG_PHY | Large Phytoplankton | inWC:1 inSed:1 | False |
| SM_PHY | Small Phytoplankton | inWC:1 inSed:1 | False |
| SM_ZOO | Small Zooplankton | inWC:1 inSed:0 | False |
| MED_ZOO | Medium Zooplankton | inWC:1 inSed:0 | False |
| LG_ZOO | Large Zooplankton | inWC:1 inSed:0 | True |
| CEP | Cephalopod | inWC:1 inSed:0 | True |
| PWN | Prawns | inWC:1 inSed:0 | True |
| PL_BACT | Pelagic Bacteria | inWC:1 inSed:0 | False |
| SED_BACT | Sediment Bacteria | inWC:0 inSed:1 | False |
| SM_INF | Small Infauna | inWC:0 inSed:1 | False |
| LG_INF | Large Infauna | inWC:0 inSed:1 | True |
| SED_EP_FF | Sediment epibenthic filter feeders | Epi | False |
| SED_EP_OTHER | Benthic grazers | Epi | True |
| MOB_EP_OTHER | Mobile epibenthic | Epi | True |
| PHYTOBEN | Phytoben | Epi | False |
| TURF | Turf algae | Epi | False |
| LAB_DET | Labile detritus | inWC:1 inSed:1 | False |
| REF_DET | Refractory detritus | inWC:1 inSed:1 | False |
| CARRION | Carrion | inWC:1 inSed:1 | False |
| MICROPHTYBENTHOS | Microphtybenthos | inWC:1 inSed:1 | False |
| DINOFLAG | Dinoflagellates | inWC:1 inSed:1 | False |
| SEAGRASS | Seagrass | Epi | False |
| FISH | Fish | inWC:0 inSed:1 | True |
| FISH_INVERT | Fished invertebrate | inWC:0 inSed:1 | True |
| MAMMAL | Mammal | inWC:0 inSed:1 | True |
| SHARK | Shark | inWC:0 inSed:1 | True |
There can only be a single instance of the following groups:
LAB_DET - Labile detritus
REF_DET - Refractory detritus
CARRION - Carrion
PL_BACT - Pelagic Bacteria
SED_BACT - Sediment Bacteria
The old codes used in Atlantis hard coded the groups in the following manner:
| Old Code | Invertebrate Type |
| CEP | CEP |
| BFS | SED_EP_FF |
| BFF | SED_EP_FF |
| BFD | SED_EP_FF |
| BG | SED_EP_OTHER |
| BMD | MOB_EP_OTHER |
| BML | MOB_EP_OTHER |
| BMS | MOB_EP_OTHER |
| PWN | PWN |
| ZL | LG_ZOO |
| BD | LG_INF |
| MA | PHYTOBEN |
| MB | MICROPHTYBENTHOS |
| SG | SEAGRASS |
| BC | LG_INF |
| ZG | LG_ZOO |
| PL | LG_PHY |
| DF | DINOFLAG |
| PS | SM_PHY |
| ZM | LG_ZOO |
| ZS | SM_ZOO |
| PB | PL_BACT |
| BB | SED_BACT |
| BO | SM_INF |
| DL | LAB_DET |
| DR | REF_DET |
| DC | CARRION |