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Merged
andybeet merged 4 commits into from
Sep 29, 2026
Merged

Modified changelog for new release 3.6723 #89

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5ad4666
Merge pull request #82 from Atlantis-Ecosystem-Model/dev
hmorzaria Sep 28, 2026
f64f4ee
Modified changelog for new release 3.6723
hmorzaria Sep 28, 2026
93cc828
Update CHANGELOG for version 3.6723
hmorzaria Sep 28, 2026
ce774e5
Update CHANGELOG with recent code modifications
hmorzaria Sep 28, 2026
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22 changes: 10 additions & 12 deletions CHANGELOG.md
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Expand Up @@ -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)

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