diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a492a0..1b2f5ae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,30 +6,28 @@ As changed, removed, or added. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## Commit [3102097](https://github.com/Atlantis-Ecosystem-Model/AtlantisTrunk/commit/310209784bb56e44980f9be6a0fc87410cb6f036) -### Changed -- Updated ReactiveAtlantisToolExample.R in the model example so it runs without having to change paths - -### Removed - -### Added -- Explicitly defined `flagmother`, `start_n`, and `end_n` in `Get_Settler_Contaminants` (atContaminants.c) to address an intermittent SETas segfault. -- Replaced `malloc` with `calloc` for `bm->forceMoveEntryInput` allocation (atForcedMovement.c) to avoid uninitialized memory. - -## Commit [cf96dbb](https://github.com/Atlantis-Ecosystem-Model/AtlantisTrunk/commit/cf96dbbb4ac7b2f3342d0caa997031f8fdaf3e29) +## [3.6723] - 2026-09-28 - Commit [5ad4666](https://github.com/Atlantis-Ecosystem-Model/AtlantisTrunk/commit/5ad46667f7977dabbeaad89ffe62e601bb1d82f4) ### Changed - Defined temp_sensitive_sp=0, salt_sensitive_sp=0, mignum_actual=0.0, and int rij, rangeid, rocstage = -1, thiscase1 = 0, thiscase2 = 0, adstage, sp_Migrate_Years, stagger_return = 0, agec; in function Ecology_Total_Verts_And_Migration in atmovement.c to correct segmentation fault - Moved /* Actual numbers returning - corrected for losses while away */ mignum_actual = MIGRATION[sp].survival[qid] * mignum; to right before mignum_actual is used for the first time +- Updated ReactiveAtlantisToolExample.R in the model example so it runs without having to change paths +- In atContaminants.c in function Change_Contaminant_Levels, separated tracking of contaminants into two distinct arrays for the organisms and the environment. +Added tracking of contaminant transfers not yet integrated into the tracer array. Applies contaminant transfer immediately to tracer arrays so that predators will see updated concentrations. +Phytoplankton, small zooplankton, filter feeders, and PWN can uptake contaminants multiple times per time step mimicking continuous feeding + ### Removed ### Added +- Explicitly defined `flagmother`, `start_n`, and `end_n` in `Get_Settler_Contaminants` (atContaminants.c) to address an intermittent SETas segfault. +- Replaced `malloc` with `calloc` for `bm->forceMoveEntryInput` allocation (atForcedMovement.c) to avoid uninitialized memory. - if (stock_id < 0) {stock_id = 0;} so stock id would be defined before bing used as it was causing a memory loss - +- Contaminants from dead organisms are transferred to Carrion in atContaminants.C. Carrion can now accumulate contaminants multiple times per timestep. +Contaminant transfer in atGroupProcesses.C to Carrion from dead organisms based on total detritus production (DL + DR) ## [3.6722] - 2026-05-22 - Commit [94ccf9b](https://github.com/Atlantis-Ecosystem-Model/AtlantisTrunk/commit/94ccf9b9b32f3465182d17645646d2c31446d95e)