From 084d8ab04df5670c72a7eebc28c66ca459e6a270 Mon Sep 17 00:00:00 2001 From: Kevin Cazelles Date: Tue, 11 Mar 2025 10:20:58 -0400 Subject: [PATCH 1/4] Remove MacOS .DS_Store file and .Rhistory --- .DS_Store | Bin 14340 -> 0 bytes atlantis/.DS_Store | Bin 32772 -> 0 bytes example/.DS_Store | Bin 10244 -> 0 bytes example/.Rhistory | 119 ------------------------------------- example/inputs/._.DS_Store | Bin 4096 -> 0 bytes 5 files changed, 119 deletions(-) delete mode 100755 .DS_Store delete mode 100755 atlantis/.DS_Store delete mode 100755 example/.DS_Store delete mode 100755 example/.Rhistory delete mode 100644 example/inputs/._.DS_Store diff --git a/.DS_Store b/.DS_Store deleted file mode 100755 index 4bb8cab192b34e1bd4b5ec9cd0e0fb1cf4970728..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 14340 zcmeHNdvFz389%>GAbZQ*W)q;WK**&L$Up)~NJ2t*+&mCMpga=tf*Nk_UC7GjZn%4s z(8g5M(iinr9ej>jsamzQjYjm_?wcxZkeK>Zi|FpJ)j@9p+a}zcOEK>Uy8CR)O_r2A3ne3S 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n~=r#3gZgjwX3N6s9bp5z@vf% z4{;q2Dz4+v;p_N!QF&~dDHpW!J{@=zzo0z*e+EdmCGzntKL2xyCVUe42pXUNr3=FU H&-wpfmduhl diff --git a/example/.Rhistory b/example/.Rhistory deleted file mode 100755 index 348f3f6..0000000 --- a/example/.Rhistory +++ /dev/null @@ -1,119 +0,0 @@ -rm(list = ls()) # clear memory -setwd("/Users/ful083/AtlantisRepository/AtlantisTrunk/example/") -library("devtools") -library("ReactiveAtlantis") -library("proj4") -####### Compare outputs and Biomass visualization ####### -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder2/outputSETAS.nc' -nc.old <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -grp.csv <- 'SETasGroupsDem.csv' -bgm.file <- 'VMPA_setas.bgm' -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -## individual file -compare(nc.current, nc.out.old = NULL, grp.csv, bgm.file, cum.depths) -## compare to previous run -compare(nc.current, nc.old, grp.csv, bgm.file, cum.depths) -####### Predation analysis from the Atlantis output ####### -biom <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASBiomIndx.txt' -diet.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASDietCheck.txt' -bio.age <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASAgeBiomIndx.txt' ## optional file. just if you want to check the predation by age -grp.csv <- 'SETasGroupsDem.csv' -## Predation by Age -predation(biom, grp.csv, diet.file, bio.age) -## No predation by Age -predation(biom, grp.csv, diet.file, bio.age = NULL) -####### Exploring predator-prey interactions from the initial conditions ####### -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -nc.initial <- 'INIT_VMPA_Jan2015.nc' -grp.csv <- 'SETasGroupsDem.csv' -bgm.file <- 'VMPA_setas.bgm' -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -feeding.mat(prm.file, grp.file, nc.initial, bgm.file, cum.depths) -####### Atlantis food web and trophic level composition ####### -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -diet.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASDietCheck.txt' -food.web(diet.file, grp.csv) -## optional you can explore the food web by polygon -food.web(diet.file, grp.file, diet.file.bypol) -## diet.file.bypol Detailed diet check file, this can be obtained as an extra output from Atlantis "DetailedDietCheck.txt". To get this file from Atlantis turn on the option "flagdietcheck" on the Run.prm file. -####### Growth of primary producers and limiting factors ####### -nc.initial <- 'INIT_VMPA_Jan2015.nc' -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -growth.pp(nc.initial, grp.csv, prm.file, nc.current) -####### Analysis of recruitment and primary production ####### -nc.initial <- 'INIT_VMPA_Jan2015.nc' -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -yoy.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASYOY.txt' -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -recruitment.cal(nc.initial, nc.current, yoy.file, grp.csv, prm.file) -####### Harvest outputs and model skill assessment ####### -catch.nc <- 'outputSETASCATCH.nc' -ext.catch <- 'external_catch_time_series.csv' -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -fsh.csv <- 'SETasFisheries.csv' -bgm.file <- 'VMPA_setas.bgm' -grp.csv <- 'SETasGroupsDem.csv' -catch(grp.csv, fsh.csv, catch.nc, ext.catch) -rm(list = ls()) # clear memory -setwd("/Users/ful083/AtlantisRepository/AtlantisTrunk/example/") -library("devtools") -library("ReactiveAtlantis") -library("proj4") -devtools::install_github('Atlantis-Ecosystem-Model/ReactiveAtlantis', force=TRUE, dependencies=TRUE) -devtools::install_github("Atlantis-Ecosystem-Model/shinyrAtlantis", force=TRUE, dependencies=TRUE) -rm(list = ls()) # clear memory -setwd("/Users/ful083/AtlantisRepository/AtlantisTrunk/example/") -library("devtools") -library("ReactiveAtlantis") -library("proj4") -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder2/outputSETAS.nc' -nc.old <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -grp.csv <- 'SETasGroupsDem.csv' -bgm.file <- 'VMPA_setas.bgm' -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -## individual file -compare(nc.current, nc.out.old = NULL, grp.csv, bgm.file, cum.depths) -## compare to previous run -compare(nc.current, nc.old, grp.csv, bgm.file, cum.depths) -biom <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASBiomIndx.txt' -diet.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASDietCheck.txt' -bio.age <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASAgeBiomIndx.txt' ## optional file. just if you want to check the predation by age -grp.csv <- 'SETasGroupsDem.csv' -## Predation by Age -## Predation by Age -predation(biom, grp.csv, diet.file, bio.age) -## No predation by Age -predation(biom, grp.csv, diet.file, bio.age = NULL) -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -nc.initial <- 'INIT_VMPA_Jan2015.nc' -grp.csv <- 'SETasGroupsDem.csv' -bgm.file <- 'VMPA_setas.bgm' -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -feeding.mat(prm.file, grp.file, nc.initial, bgm.file, cum.depths) -feeding.mat(prm.file, grp.csv, nc.initial, bgm.file, cum.depths) -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -diet.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASDietCheck.txt' -food.web(diet.file, grp.csv) -nc.initial <- 'INIT_VMPA_Jan2015.nc' -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -growth.pp(nc.initial, grp.csv, prm.file, nc.current) -nc.initial <- 'INIT_VMPA_Jan2015.nc' -nc.current <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETAS.nc' -yoy.file <- '/Users/ful083/AtlantisRepository/AtlantisTrunk/example/outputFolder/outputSETASYOY.txt' -grp.csv <- 'SETasGroupsDem.csv' -prm.file <- 'VMPA_setas_biol_fishing_Trunk.prm' -recruitment.cal(nc.initial, nc.current, yoy.file, grp.csv, prm.file) -catch.nc <- 'outputSETASCATCH.nc' -ext.catch <- 'external_catch_time_series.csv' -cum.depths <- c(0,20,50,100,250,700,2000) ## This should be the cummulative depth of your model -fsh.csv <- 'SETasFisheries.csv' -bgm.file <- 'VMPA_setas.bgm' -grp.csv <- 'SETasGroupsDem.csv' -catch(grp.csv, fsh.csv, catch.nc, ext.catch) diff --git a/example/inputs/._.DS_Store b/example/inputs/._.DS_Store deleted file mode 100644 index 338bd7ba27b62046d75470a7732f6f1b01806cb5..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4096 zcmZQz6=P>$Vqox1Ojhs@R)|o50+1L3ClDJkFz{^v(m+1nBL)UWIUpMh9H2BNBh0QSWmV*mgE From 5e171f0743e476bf458ab235ce71d25b1ff0fef9 Mon Sep 17 00:00:00 2001 From: Kevin Cazelles Date: Tue, 11 Mar 2025 10:47:23 -0400 Subject: [PATCH 2/4] Fix BiTAC_sp memory allocation --- atlantis/atmanage/atManageSetup.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/atlantis/atmanage/atManageSetup.c b/atlantis/atmanage/atManageSetup.c index 5741bf4..2de15a7 100755 --- a/atlantis/atmanage/atManageSetup.c +++ b/atlantis/atmanage/atManageSetup.c @@ -1189,7 +1189,7 @@ void Allocate_Arrays_Pre_Load(MSEBoxModel *bm) { /* These are always allocated even if the management option is off */ bm->reg_season = (int *) i_alloc1d(bm->K_num_reg); bm->phased_out = Util_Alloc_Init_2D_Double(nfleets, bm->K_num_tot_sp, 1.0); - bm->BiTAC_sp = (double ****) alloc4d(2, bm->K_num_tot_sp, totalreg_id + 1, 6); + bm->BiTAC_sp = (double ****) alloc4d(2, totalreg_id + 1, bm->K_num_tot_sp, 6); bm->BiTACamt = Util_Alloc_Init_4D_Double(2, nfleets, bm->K_num_tot_sp, 6, 0.0); bm->TACamt = Util_Alloc_Init_3D_Double(K_num_TAC_entries, nfleets, bm->K_num_tot_sp, 0.0); bm->TripCatch = Util_Alloc_Init_2D_Double(nfleets, bm->K_num_tot_sp, 0.0); From b54ffd163e562961ce02dab52d4ab54bd6de76b4 Mon Sep 17 00:00:00 2001 From: Kevin Cazelles Date: Tue, 11 Nov 2025 13:14:30 -0500 Subject: [PATCH 3/4] remove all .DS_Store --- .gitignore | 4 ---- atlantis/atecology/.DS_Store | Bin 6148 -> 0 bytes atlantis/ateconomic/.DS_Store | Bin 6148 -> 0 bytes atlantis/atlantismain/.DS_Store | Bin 6148 -> 0 bytes atlantis/atmanage/.DS_Store | Bin 6148 -> 0 bytes .../win32_vs_dll_4.0.1-beta3.tar/.DS_Store | Bin 6148 -> 0 bytes example/inputs/.DS_Store | Bin 10244 -> 0 bytes example/outputFolderPristine/.DS_Store | Bin 6148 -> 0 bytes 8 files changed, 4 deletions(-) delete mode 100755 atlantis/atecology/.DS_Store delete mode 100755 atlantis/ateconomic/.DS_Store delete mode 100755 atlantis/atlantismain/.DS_Store delete mode 100755 atlantis/atmanage/.DS_Store delete mode 100755 atlantis/externalLibs/win32_vs_dll_4.0.1-beta3.tar/.DS_Store delete mode 100755 example/inputs/.DS_Store delete mode 100755 example/outputFolderPristine/.DS_Store diff --git a/.gitignore b/.gitignore index f91e7e5..d548d16 100644 --- a/.gitignore +++ b/.gitignore @@ -16,10 +16,6 @@ autom4te.cache/ *atlantisMerged *atlantisMerged.pc .DS_Store -atlantis/.DS_Store -.DS_Store -.DS_Store Trunk2025.xcworkspace/xcuserdata/ful083.xcuserdatad/UserInterfaceState.xcuserstate -.DS_Store Trunk2025.xcworkspace/xcuserdata/ful083.xcuserdatad/UserInterfaceState.xcuserstate .Rproj.user/ diff --git a/atlantis/atecology/.DS_Store b/atlantis/atecology/.DS_Store deleted file mode 100755 index b0fcd993d245db0f556919fd36418f4a18b549e1..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHKxlRKy5PgOekq}Z!N`CdIsC!Kt?kt!z$0JJIpvDtkdlIdqN^0NMnqOG;YW)lB z;&xfjPMfMO>2-)JRJi93D~$1g26OD;2nU=UbI)^TS?Jy?oYQYf4l3rXi6!28ye_G4 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22:03:36 +1000 Subject: [PATCH 4/4] Update BiTAC_sp in atManageSetup.c Fixed BiTAC_sp with Util_Alloc_Init_4D_Double instead for consistency sake --- atlantis/atmanage/atManageSetup.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/atlantis/atmanage/atManageSetup.c b/atlantis/atmanage/atManageSetup.c index a013293..5bc8bc5 100755 --- a/atlantis/atmanage/atManageSetup.c +++ b/atlantis/atmanage/atManageSetup.c @@ -1193,7 +1193,7 @@ void Allocate_Arrays_Pre_Load(MSEBoxModel *bm) { /* These are always allocated even if the management option is off */ bm->reg_season = (int *) i_alloc1d(bm->K_num_reg); bm->phased_out = Util_Alloc_Init_2D_Double(nfleets, bm->K_num_tot_sp, 1.0); - bm->BiTAC_sp = (double ****) alloc4d(2, totalreg_id + 1, bm->K_num_tot_sp, 6); + bm->BiTAC_sp = Util_Alloc_Init_4D_Double(2, bm->K_num_tot_sp, totalreg_id + 1, 6, 0.0);; bm->BiTACamt = Util_Alloc_Init_4D_Double(2, nfleets, bm->K_num_tot_sp, 6, 0.0); bm->TACamt = Util_Alloc_Init_3D_Double(K_num_TAC_entries, nfleets, bm->K_num_tot_sp, 0.0); bm->TripCatch = Util_Alloc_Init_2D_Double(nfleets, bm->K_num_tot_sp, 0.0);