v6698
New parameters to add ****biology.prm**** Flags to activate temperature dependent movement and recruitment
flagtempdepend_move 0 flagtempdepend_reprod 0
****run.prm**** Flag is used to maintain old plankton mortality assumptions (from very early code versions that persisted as potential bug into newer models). Turning it on zeroes out phytoplankton mortality and only allows for lysis in phytoplankton. Note: Testing this flag using the Puget Sound model found no difference in output between 0 and 1 settings
flag_replicated_old_PPmort 0
****harvest.prm**** Related to companion species. Catch of one species results in bycatch of another
K_max_sp_co 0 max_co_sp_XXX 0
****migrations.csv**** One additional column is required (17 columns total)
ReprodAllowed is whether individuals participating in this migration can spawn when they reach maturity (1 = yes, 0 = no). If set to 0 then in multi-year spawners (like salmon), the individuals will not spawn even if they reach adult ages during that migration.
SVN commit message
Changed paths: M /Atlantis/trunk/atlantis/PreRules.am M /Atlantis/trunk/atlantis/atecology/atbiology.c M /Atlantis/trunk/atlantis/atecology/atbiolsetup.c M /Atlantis/trunk/atlantis/atecology/atdemography.c M /Atlantis/trunk/atlantis/atecology/atmovement.c M /Atlantis/trunk/atlantis/atlantismain/atlantismain.c M /Atlantis/trunk/atlantis/atlantismain/include/atlantisboxmodel.h M /Atlantis/trunk/atlantis/atmanage/atManage.c M /Atlantis/trunk/atlantis/atmanage/atRlinkRAssess.c M /Atlantis/trunk/atlantis/atphysics/attracerIO.c M /Atlantis/trunk/example/VMPA_setas_run_fishing_F_Trunk.prm
Fixed some compile issues for Sonoma M2 Macs, added more to tiered management code and corrected invertebrate movement memory bug
Atlantis model used: Atlantis Model for Puget Sound https://github.com/hmorzaria/psatlantismodel commit 87031b7
Atlantis revision comments
Version 6698
Date pulled: November 28, 2023
OS: Ubuntu 20.04 LTS
Environment: Linux
Modeler: Hem Nalini Morzaria-Luna
Notes
Model behavior