Atlantis-Ecosystem-Model · hmorzaria · May 28, 2026 · Mar 11, 2025 · Mar 11, 2025 · Nov 11, 2025
diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/build_run_SETAS1.yml b/.github/workflows/build_run_SETAS1.yml
@@ -45,7 +45,7 @@ jobs:
           TZ=America/New_York &&
           ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone &&
           apt-get update && 
-          apt-get install  -yq build-essential autoconf libnetcdf-dev libxml2-dev libproj-dev subversion valgrind dos2unix gawk nano r-base &&
+          apt-get install  -yq build-essential autoconf libnetcdf-dev libxml2-dev libproj-dev subversion valgrind dos2unix gawk nano r-base git &&
           cd atlantis && aclocal && autoheader && autoconf && automake -a && ./configure --enable-rassesslink && make && make install &&
           echo 'Now run the model!' &&
           cd ../example &&

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,31 +1,54 @@
 # Changelog
 
 All notable changes to this repository will be documented in this file.
-As changed, removed or added.
+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).
 
-## [3.6721.1] - 2026-04-21 
+## [3.6722] - 2026-05-22 - Commit 
+
 ### Added
-Created md file with a table listing Atlantis models in use, location, and contact person
-GitHub actions to build and run SETAS when a pull request is triggered
-Templates for bug reporting, feature requests and pull requests that standardize content for maintainers and reviewers. 
+- Created md file with a table listing Atlantis models in use, location, and contact person
+- GitHub actions to build and run SETAS when a pull request is triggered
+- Templates for bug reporting, feature requests and pull requests that standardize content for maintainers and reviewers. 
+- Parameter min_pool_cont for the Contaminant module, which sets the threshold for minimum contaminant concentration. This addition decouples min_pool a global parameter from the contaminant submodule. Need to add min_pool_cont as a parameter if using track_contaminants 
+- Instructions to add new features or bug fixes to the user manual. The documentation should be updated directly after the feature or bug is incorporated in a new release
+- Code to identify the Git release and return the release version
+- mFC fisheries produce no harvest when flagdisplace is on. The Effort array is used as a scalar multiplier for mFC catch but was initialized to 0.0 instead of 1.0. Added flagMFCdisplace_id to identify mFC fisheries and initialize their Effort to 1.0. Modified the fishery activation check to prevent mFC fisheries with displacement from being skipped. Files: atlantisboxmodel.h, atManageSetup.c, atManage.c
+
 
 ### Changed
-In atlantis/PreRules.am‎ refactors the code to detect the underlying OS and then "turn" on the appropriate flag
+- In atlantis/PreRules.am‎ refactors the code to detect the underlying OS and then "turn" on the appropriate flag
+- Readme and CHANGELOG are updated
+- CumDisplaceEffort accumulation was in dead code path. Accumulation was in the if(!bm->EffortModelsActive) block, but EffortModelsActive is true when any fishery has flageffortmodel > 0 (including forced effort = 11). Placed accumulation in the EffortModelsActive code path instead.
+File: atManage.c
+- Wrong box index for MPA scaling in readts_effort branch. MPA scale was read from bm->MPA[bm->current_box][fishery_id] instead of bm->MPA[ij][fishery_id]. current_box was always 0, so every box got box 0's MPA value. Changed to bm->MPA[ij][fishery_id].
+File: atManage.c
+- orig_FCpressure set after MPA scaling instead of before. In the readts_effort branch, orig_FCpressure was assigned after FCpressure *= mpa_scale, so Effort_Displacement computed orig_FCpressure - FCpressure = 0. Set orig_FCpressure before MPA scaling.
+File: atManage.c
+- All displacement logic was gated by TempCPUE < mEff_thresh. For readts_effort fisheries, TempCPUE is never calculated (stays 0.0), and with mEff_thresh = 0.0 the condition 0.0 < 0.0 is false. The manual (Section 15.6.1) states displacement should occur both for low CPUE and when MPAs are imposed. Added MPA as alternative trigger: if ((TempCPUE < mEff_thresh) || (MPA[ij][fishery_id] < 1.0)). File: atManage.c (Effort_Displacement function)
+- Inverted MPA check in displacement destination scoring. Adjacent boxes were scored using MPA_check = 1.0 - bm->MPA[nb][fishery_id]. For open boxes (MPA=1.0) this gives 0.0, zeroing out their biomass attractiveness. Changed to MPA_check = bm->MPA[nb][fishery_id] so open boxes retain full attractiveness.
+File: atManage.c (Effort_Displacement function)
+- Biomass comparison blocked MPA-imposed displacement. Displacement was conditional on maxfishthere > fishhere. Closed MPA boxes can have high target biomass, causing this condition to fail. The manual states displacement "will still occur" when MPAs are imposed. Separated MPA-imposed displacement (unconditional, find best open neighbour) from CPUE-triggered displacement (conditional on better biomass elsewhere). File: atManage.c (Effort_Displacement function)
+- Renamed output file from OutDisplaceEffort.txt to OutDetailedEffort.txt (atHarvestIO.c)
+- Detailed in the following Google group thread: https://groups.google.com/g/atlantis-ecosystem-model/c/gNJN6AXaM88, the way the allocation is done does not match the way BiTAC_sp is used. For instance:
+AtlantisTrunk/atlantis/atmanage/atManage.c. Line 2382 in 9f99af0, bm->BiTAC_sp[bim][nreg][sp][now_id] = 0.0; shows that the second dimension is nreg, but the allocation used the number of species for the second dimension.
+- SVN release number was printed in log file. This has been replaced by GitHub version release in an earlier PR. For this to work git is required as a system dependency. This will not work for the SETAS workflow. This version number also needs to be printed to standard out. This PR fixes the standard out printing
 
 ### Removed 
-Extra printfs in atUtils.c used for debugging 
-Extra printfs in atbiology.c that was creating a memory error
-atbiology.c
+- Extra printfs in atUtils.c used for debugging 
+- Extra printfs in atbiology.c that was creating a memory error
+- atbiology.c
 	//printf("printing tracer\n");
 	//printf("WC - %d, box: %d, layer: %d, %s - bm->atEcologyModule->localTracer[i] = %.20e, fluxFlag = %d\n",i, bm->current_box, bm->current_layer, Varname[i], localWCTracers[i], Fluxflag[i]);
+- Rremove .DS_Store files and .Rhistory. .DS_Store are in the .gitignore but once they are tracked they need to be removed explicitly (https://docs.github.com/en/get-started/git-basics/ignoring-files).
+- Existing quit statement in at_demography.c for when maternal transfer was on and had externally reproducing species , but the necessary code has been added and the quit statement is no longer necessary
 
 ## [3.6721] - 2026-01-12 - Commit 51f186d
 
 ### Added
-Missing lines in Free_Contaminants in atContaminant.c 
+- Missing lines in Free_Contaminants in atContaminant.c 
 	    free(bm->contaminantStructure[cIndex]->sp_avoid);
         free(bm->contaminantStructure[cIndex]->sp_K_avoid);
         free(bm->contaminantStructure[cIndex]->sp_L);

diff --git a/atlantis/.DS_Store b/atlantis/.DS_Store
diff --git a/atlantis/ConvertAtlantis/Makefile.in b/atlantis/ConvertAtlantis/Makefile.in
@@ -282,6 +282,7 @@ PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+RELEASE_VERSION = @RELEASE_VERSION@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -367,7 +368,10 @@ GCCVERSION = $(shell gcc --version | grep ^gcc | sed 's/^.* //g')
 #-Wconversion
 WARN = -Wall -Wextra -Wno-unused-parameter -Wuninitialized \
 	-Warray-bounds $(am__append_1)
-AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN)
+
+#fetching repo version from git
+AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN) \
+	-DRELEASE_VERSION=\"$(RELEASE_VERSION)\"
 lib_LIBRARIES = libatConvertAtlantis.a
 libatConvertAtlantis_adir = $(includedir)/ConvertAtlantis
 libatConvertAtlantis_a_SOURCES = atBioltoXML.c atCreateXML.c convertXML.h atHarvesttoXML.c atManagetoXML.c atImplementationtoXML.c atAssesstoXML.c \

diff --git a/atlantis/Makefile.in b/atlantis/Makefile.in
@@ -252,6 +252,7 @@ PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+RELEASE_VERSION = @RELEASE_VERSION@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@

diff --git a/atlantis/atCLAMLink/Makefile.in b/atlantis/atCLAMLink/Makefile.in
@@ -280,6 +280,7 @@ PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+RELEASE_VERSION = @RELEASE_VERSION@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -365,7 +366,10 @@ GCCVERSION = $(shell gcc --version | grep ^gcc | sed 's/^.* //g')
 #-Wconversion
 WARN = -Wall -Wextra -Wno-unused-parameter -Wuninitialized \
 	-Warray-bounds $(am__append_1)
-AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN)
+
+#fetching repo version from git
+AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN) \
+	-DRELEASE_VERSION=\"$(RELEASE_VERSION)\"
 lib_LIBRARIES = libatCLAMLink.a
 c_sources = atCLAMManage.c atCLAMLinkIO.c atCLAMComm.c atCLAMLinkSetup.c atCLAMImplement.c
 h_sources = $(top_srcdir)/atCLAMLink/include/atCLAMLink.h  

diff --git a/atlantis/atSS3Link/Makefile.in b/atlantis/atSS3Link/Makefile.in
@@ -280,6 +280,7 @@ PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+RELEASE_VERSION = @RELEASE_VERSION@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -365,7 +366,10 @@ GCCVERSION = $(shell gcc --version | grep ^gcc | sed 's/^.* //g')
 #-Wconversion
 WARN = -Wall -Wextra -Wno-unused-parameter -Wuninitialized \
 	-Warray-bounds $(am__append_1)
-AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN)
+
+#fetching repo version from git
+AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN) \
+	-DRELEASE_VERSION=\"$(RELEASE_VERSION)\"
 lib_LIBRARIES = libatSS3Link.a
 c_sources = atSS3Link.c atSS3LinkIO.c atSS3DataGen.c atSS3Util.c atCloseKin.c 
 

diff --git a/atlantis/atassess/Makefile.in b/atlantis/atassess/Makefile.in
@@ -282,6 +282,7 @@ PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+RELEASE_VERSION = @RELEASE_VERSION@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -367,7 +368,10 @@ GCCVERSION = $(shell gcc --version | grep ^gcc | sed 's/^.* //g')
 #-Wconversion
 WARN = -Wall -Wextra -Wno-unused-parameter -Wuninitialized \
 	-Warray-bounds $(am__append_1)
-AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN)
+
+#fetching repo version from git
+AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN) \
+	-DRELEASE_VERSION=\"$(RELEASE_VERSION)\"
 lib_LIBRARIES = libatassess.a
 libatassess_adir = $(includedir)/atassess
 libatassess_a_SOURCES = atclassical.c atindices.c atsample.c atsurvey.c \

diff --git a/atlantis/atbrokerlink/Makefile.in b/atlantis/atbrokerlink/Makefile.in
@@ -276,6 +276,7 @@ PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+RELEASE_VERSION = @RELEASE_VERSION@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -361,7 +362,10 @@ GCCVERSION = $(shell gcc --version | grep ^gcc | sed 's/^.* //g')
 #-Wconversion
 WARN = -Wall -Wextra -Wno-unused-parameter -Wuninitialized \
 	-Warray-bounds $(am__append_1)
-AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN)
+
+#fetching repo version from git
+AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN) \
+	-DRELEASE_VERSION=\"$(RELEASE_VERSION)\"
 lib_LIBRARIES = libbrokerlink.a
 libbrokerlink_adir = $(includedir)/atbrokerlink
 libbrokerlink_a_SOURCES = requests.pb-c.h requests.pb-c.c responses.pb-c.h responses.pb-c.c \

diff --git a/atlantis/atecology/.DS_Store b/atlantis/atecology/.DS_Store
diff --git a/atlantis/atecology/Makefile.in b/atlantis/atecology/Makefile.in
@@ -307,6 +307,7 @@ PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+RELEASE_VERSION = @RELEASE_VERSION@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -392,7 +393,10 @@ GCCVERSION = $(shell gcc --version | grep ^gcc | sed 's/^.* //g')
 #-Wconversion
 WARN = -Wall -Wextra -Wno-unused-parameter -Wuninitialized \
 	-Warray-bounds $(am__append_1)
-AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN)
+
+#fetching repo version from git
+AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN) \
+	-DRELEASE_VERSION=\"$(RELEASE_VERSION)\"
 lib_LIBRARIES = libatecology.a
 libatecology_adir = $(includedir)/atecology
 libatecology_a_SOURCES = atbiolUtil.c atannualbiology.c atbiolmessage.c atbiology.c atbiolsetup.c \