From f64f4ee0899bd7b0e09a27d68da02edee4b25796 Mon Sep 17 00:00:00 2001 From: hmorzaria Date: Mon, 28 Sep 2026 23:49:39 +0000 Subject: [PATCH 1/3] Modified changelog for new release 3.6723 --- CHANGELOG.md | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a492a0..4c6943b 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/94ccf9b9b32f3465182d17645646d2c31446d95e) ### 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) From 93cc828a20c5aceb52d3c36247125989e119199c Mon Sep 17 00:00:00 2001 From: Hem Nalini Morzaria-Luna Date: Mon, 28 Sep 2026 16:54:58 -0700 Subject: [PATCH 2/3] Update CHANGELOG for version 3.6723 Updated the commit reference for version 3.6723 and added new variable definitions. Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c6943b..ed689bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ 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). -## [3.6723] - 2026-09-28 - Commit [5ad4666](https://github.com/Atlantis-Ecosystem-Model/AtlantisTrunk/commit/94ccf9b9b32f3465182d17645646d2c31446d95e) +## [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; From ce774e5a88bbcff18c4f39ac4086ee1c032cac31 Mon Sep 17 00:00:00 2001 From: Hem Nalini Morzaria-Luna Date: Mon, 28 Sep 2026 16:55:56 -0700 Subject: [PATCH 3/3] Update CHANGELOG with recent code modifications Updated changelog for correct file name Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ed689bc..1b2f5ae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ in function Ecology_Total_Verts_And_Migration in atmovement.c to correct segment - 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. +- 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