Use all survey data, added conditional macros

PreProcess/HabCamData5mmbin.m

@@ -139,7 +139,7 @@ function HabCamData5mmbin(refYear, domain, appendResults)
         % accumulate 15 to 18
         % sum n(k+24) - n(k+30) into k=25
         region = GetRegion(isOctave, lat_t(k,:), lon_t(k,:), stratum_t(k,:));
-        if region>0
+        if region >= 0  % TODO filtering does not match recruit as it does no filtering, use all regions
             if isOctave
                 k25 = sum((M(n(k)+24:n(k)+30, svCol)));
                 density = [(M(n(k):n(k)+23, svCol));k25];

PreProcess/ProcessRecruitData.m

@@ -81,7 +81,7 @@ function ProcessRecruitData(yrStart, yrEnd, domain)
 flnm='Data/RecruitsUnadjusted.csv';
 header='"decimal year", "latitude", "longitude", "UTM x", "UTM y", "bottom depth(m)","recruits per m^2"';
 fprintf('Writing to %s\n\n', flnm)
-writecsv(M,flnm,['%g, %g, %g, %g, %g, %g, %e'],header);
+writecsv(M,flnm,['%f, %f, %f, %f, %f, %f, %e'],header);
 
 
 %XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
@@ -157,7 +157,7 @@ function ProcessRecruitData(yrStart, yrEnd, domain)
 M=M(j,:);
 flnm='Data/RecruitsRockStrataAdjustment.csv';
 header='"decimal year", "latitude", "longitude", "UTM x", "UTM y","bottom depth(m)","recruits per sq m raw","Is Rock Strata","recruits per sq m adjusted"';
-writecsv(M,flnm,['%g, %g, %g, %g, %g, %g, %e, %i ,%e' ],header);
+writecsv(M,flnm,['%f, %f, %f, %f, %f, %f, %e, %i ,%e' ],header);
 fprintf('Writing to %s\n\n', flnm)
 
 close all;
@@ -220,7 +220,7 @@ function ProcessRecruitData(yrStart, yrEnd, domain)
 flnm=['Data/Recruits', domain, '.csv'];
 header='"decimal year", "utm x", "utm y", "bottom depth(m)","recruits per sq m"';
 fprintf('Writing to %s\n', flnm)
-writecsv(M,flnm,'%g, %f, %f, %f, %e',header);
+writecsv(M,flnm,'%f, %f, %f, %f, %e',header);
 
 fprintf('Reading from %s\n', flnm);
 if isOctave
@@ -242,7 +242,7 @@ function ProcessRecruitData(yrStart, yrEnd, domain)
         end
         flnm=['Data/Recruits',int2str(yr),domain,'.csv'];
         header='"decimal year", "utm x", "utm y", "bottom depth(m)","recruits per sq m"';
-        writecsv(M,flnm,'%g, %f, %f, %f, %e',header);
+        writecsv(M,flnm,'%f, %f, %f, %f, %e',header);
         fprintf('Writing to %s. Number of records %d\n', flnm, size(M,1))
     end
 else

PythonScripts/GUI/GeoSAM/GeoSams.py

@@ -74,7 +74,7 @@
 #  arg#        1     2              3                  4                   5
 def Interpolate(ukCfgFile, domainName, obsFile, gridFile, zArg, procID, retDict):
     ex = os.path.join('UKsrc', 'UK')
-    outputFile = 'proc_' + obsFile + '_' + str(procID) +'.txt'
+    outputFile = 'proc_' + obsFile + '_' + str(procID).zfill(3) +'.txt'
     cmd = [ex, ukCfgFile, domainName, obsFile + '.csv', gridFile, zArg]
     with open(outputFile, "w") as outfile:
         result = subprocess.run(cmd, stdout=outfile)

PythonScripts/GUI/GeoSAM/MainInputFrame.py

@@ -86,7 +86,7 @@ def __init__(self, container, friend, tsPerYear, selectedOutputs, maxYears):
         # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
         survDataFrame = ttk.LabelFrame(self, text='Survey Data Files, Environment Variables', style='SAMS.TFrame')
         self.dredgeDataFile = SubFrameElement(self, survDataFrame, 'Dredge Survey Data File', 'dredgetowbysize7917',  0, 0, 1, width=35)
-        self.habCamDataFile = SubFrameElement(self, survDataFrame, 'HabCam Survey Data File', 'Habcam_BySegment_2000_2011-2023',1, 0, 1, width=35)
+        self.habCamDataFile = SubFrameElement(self, survDataFrame, 'HabCam Survey Data File', 'Habcam_BySegment_2000_2011-2023_v2',1, 0, 1, width=35)
         #-------------------------------------------------------------------------------------------
         self.setDredgeDataButton = ttk.Button(survDataFrame, text='Set DredgeData', style="BtnBluGrn.TLabel", command=self.SetDredgeFileName)
         self.setDredgeDataButton.grid(row=0, column=3)

SRC/IORoutines.f90

@@ -303,43 +303,6 @@ subroutine Write_Column_CSV(n,f,header,file_name,append)
 
 endsubroutine Write_Column_CSV
 
-!--------------------------------------------------------------------------------------------------
-!--------------------------------------------------------------------------------------------------
-!subroutine Write_CSV_H(n,m,f,file_name,nndim)
-! Purpose: Write values of a matrrix (f) to a csv file in exponential format.
-! Inputs:
-!  n (integer) number of rows in f 
-!  m (integer) number of columns in f
-! f (real(dp)) values to write to csv file
-! file_name (character(72)) filename to write f to in csv format
-!--------------------------------------------------------------------------------------------------
-! Keston Smith (IBSS corp) June-July 2021
-!--------------------------------------------------------------------------------------------------
-subroutine Write_CSV_H(n,m,f,file_name,nndim,header)
-    use globals
-    implicit none
-    integer, intent(in):: n,m,nndim
-    real(dp), intent(in):: f(nndim,*)
-    character(*), intent(in)::file_name,header
-    integer  k
-    character(fname_len) buf,fmtstr
-    k=m-1
-    write(buf,'(I6)')k
-    !
-    ! format for exponential format
-    !
-    fmtstr='('//trim(adjustl(buf))//'(ES14.7 : ", ") (ES14.7 : ))'
-    !fmtstr='('//trim(adjustl(buf))//'(E : ", ") (E : ))'
-    open(write_dev,file=file_name)
-    write(write_dev,'(A)') trim(adjustl( header))
-    do k=1,n
-    !write(write_dev,trim(fmtstr)) f(k,1:m)
-    write(write_dev,fmtstr) f(k,1:m)
-    enddo
-    close(write_dev)
-endsubroutine Write_CSV_H
-!--------------------------------------------------------------------------------------------------
-
 
 !--------------------------------------------------------------------------------------------------
 ! subroutine Read_CSV

SRC/ScallopMortality.f90

@@ -134,8 +134,13 @@ module Mortality_Mod
 real(dp), PRIVATE, allocatable :: F_mort(:)
 real(dp), PRIVATE, allocatable :: landings_by_num(:)
 real(dp), PRIVATE, allocatable :: landings_wgt_grams(:)
-real(dp), PRIVATE, allocatable :: lpue(:) !, dredge_time(:), dredge_area(:)
+real(dp), PRIVATE, allocatable :: lpue(:)
 real(dp), PRIVATE, allocatable :: fishing_effort(:)
+#ifdef ACCUM_LANDINGS
+real(dp), PRIVATE, allocatable :: landings_accum(:)
+real(dp), PRIVATE, allocatable :: landings_wgt_accum(:)
+real(dp), PRIVATE, allocatable :: lpue_accum(:)
+#endif
 
 real(dp), PRIVATE :: expl_scallops_psqm_at_size(num_size_classes)
 real(dp), PRIVATE :: landings_at_size(num_size_classes)
@@ -161,8 +166,11 @@ subroutine Destructor()
 
     deallocate(landings_by_num)
     deallocate(landings_wgt_grams)
-    deallocate(lpue) !, dredge_time, dredge_area)
+    deallocate(lpue)
     deallocate(fishing_effort)
+#ifdef ACCUM_LANDINGS
+    deallocate(landings_accum, landings_wgt_accum, lpue_accum)
+#endif
 endsubroutine Destructor
 
 !==================================================================================================================
@@ -232,12 +240,25 @@ subroutine Set_Mortality(mortality, grid, shell_lengths, dom_name, dom_area, num
     allocate(expl_scallops_psqm(num_grids))
     allocate(expl_num(num_grids))
     allocate(F_mort(num_grids))
-    allocate(lpue(num_grids)) !, dredge_time(num_grids), dredge_area(num_grids))
+    allocate(lpue(num_grids))
     allocate(fishing_effort(num_grids))
 
     allocate(landings_by_num(num_grids))
     allocate(landings_wgt_grams(num_grids))
+#ifdef ACCUM_LANDINGS
+    allocate(landings_wgt_accum(num_grids), lpue_accum(num_grids), landings_accum(num_grids))
 
+    landings_accum(:) = 0.D0
+    landings_wgt_accum(:) = 0.D0
+    lpue_accum(:) = 0.D0
+#endif
+
+
+#ifdef ACCUM_LANDINGS
+    write(*,*) term_yel, 'Mortality: Accumulating landing values', term_blk
+#else
+    write(*,*) term_yel, 'Mortality: Landing values at timestep', term_blk
+#endif
     !---------------------------------------------------
     ! Set mortality parameters
     !---------------------------------------------------
@@ -425,32 +446,32 @@ function Set_Fishing_Effort(year, ts, state_mat, weight_grams, mortality, grid)
 
     !call  Calc_LPUE(expl_biomass_gpsqm, expl_scallops_psqm, lpue, dredge_time, dredge_area)
     lpue = Calc_LPUE(expl_biomass_gpsqm, expl_scallops_psqm)
+#ifdef ACCUM_LANDINGS
+    lpue_accum(:) = lpue_accum(:) + lpue(:)
+#endif
 
-    c_mort = fishing_mort * sum(expl_num(:)) / dot_product(expl_num(:), lpue(:)**alpha_mort) 
+    c_mort = fishing_mort * sum(expl_biomass_gpsqm(:)) / dot_product(expl_biomass_gpsqm(:), lpue(:)**alpha_mort) 
     F_mort(:) = c_mort * lpue(:)**alpha_mort
     F_mort(:) = Set_Fishing_Mortality(grid(1:num_grids), year, .true., F_mort(:))
 
     do loc = 1, num_grids
 
         ! (1._dp - exp(-F * delta_time)) * state * grid_area_sqm  * selectivity
         landings_at_size(:) = (1._dp - exp(-F_mort(loc) * delta_time)) &
-        &    * state_mat(loc, 1:num_size_classes) * grid_area_sqm&
-        &    * mortality(loc)%selectivity(1:num_size_classes)
+        &    * state_mat(loc, :) * grid_area_sqm * mortality(loc)%selectivity(:)
 
         ! (1._dp - exp(-F * delta_time))
         ! * dot_product(selectivity * state * grid_area_sqm, weight)
-        landings_wgt_grams(loc)        =&
-        &    dot_product(landings_at_size(:),        weight_grams(loc,1:num_size_classes))
-
+        landings_wgt_grams(loc) = dot_product(landings_at_size(:), weight_grams(loc,:))
+
         ! (1._dp - exp(-F * delta_time)) * selectivity * state * grid_area_sqm
         landings_by_num(loc) = sum(landings_at_size(:))
-    enddo
-
-    !=============================================================
-    ! originally in metric tons, Set_Fishing_Effort_Weight_xx modified to accept grams
-    total_catch = sum(landings_wgt_grams)
-    !=============================================================
 
+#ifdef ACCUM_LANDINGS
+        landings_wgt_accum(loc) = landings_wgt_accum(loc) + landings_wgt_grams(loc)
+        landings_accum(loc) = landings_accum(loc) + landings_by_num(loc)
+#endif
+    enddo
 
     ! Report current timestep results
     call Mortality_Write_At_Timestep(year, ts, state_mat, weight_grams, mortality, grid)
@@ -467,6 +488,7 @@ function Set_Fishing_Effort(year, ts, state_mat, weight_grams, mortality, grid)
             endif
         enddo
         ! 
+        total_catch = sum(landings_wgt_grams)
         if (expl_scallops_psqm(loc) .EQ. 0._DP) then
             ! if expl_scallops_psqm(n) is 0 then stands to reason that there would 
             ! be zero biomass as well and thus no fishing effort.
@@ -838,18 +860,34 @@ subroutine Mortality_Write_At_Timestep(year, ts, state_mat, weight_grams, mortal
 &    call Write_Column_CSV(num_grids, F_mort(1:num_grids), 'FMORT',&
 &    output_dir//'Lat_Lon_Surv_FMOR_'//domain_name//'.csv',.true.)
 
+! landings_accum or landings_by_num
+! landings_wgt_accum or landings_wgt_grams
+! lpue_accum or lpue
+#ifdef ACCUM_LANDINGS
+if (data_select%plot_LAND) &
+&    call Write_Column_CSV(num_grids, landings_accum(:), 'Landings', & 
+&    output_dir//'Lat_Lon_Surv_LAND_'//domain_name//'.csv',.true.)
+
+if (data_select%plot_LNDW) & 
+&    call Write_Column_CSV(num_grids, landings_wgt_accum(:), 'LNDW', & 
+&    output_dir//'Lat_Lon_Surv_LNDW_'//domain_name//'.csv',.true.)
+
+if (data_select%plot_LPUE) &
+&    call Write_Column_CSV(num_grids, lpue_accum(:), 'LPUE',&          
+&    output_dir//'Lat_Lon_Surv_LPUE_'//domain_name//'.csv',.true.)
+#else
 if (data_select%plot_LAND) &
 &    call Write_Column_CSV(num_grids, landings_by_num(:), 'Landings', &
 &    output_dir//'Lat_Lon_Surv_LAND_'//domain_name//'.csv',.true.)
 
-if (data_select%plot_LNDW) &
+if (data_select%plot_LNDW) & 
 &    call Write_Column_CSV(num_grids, landings_wgt_grams(:), 'LNDW', &
 &    output_dir//'Lat_Lon_Surv_LNDW_'//domain_name//'.csv',.true.)
 
 if (data_select%plot_LPUE) &
 &    call Write_Column_CSV(num_grids, lpue(:), 'LPUE',&
 &    output_dir//'Lat_Lon_Surv_LPUE_'//domain_name//'.csv',.true.)
-
+#endif
 ! write annual results, i.e. every ts_per_year
 ! This data is later interpolated to MA or GB Grid
 if (mod(ts, ts_per_year) .eq. 1) then
@@ -879,6 +917,28 @@ subroutine Mortality_Write_At_Timestep(year, ts, state_mat, weight_grams, mortal
     &    call Write_Column_CSV_By_Region(num_grids, F_mort(:), grid(1:num_grids)%lon, 'FMOR', &
     &    data_dir//'X_Y_FMOR_'//domain_name//trim(buf), .true.)
 
+! landings_accum or landings_by_num
+! landings_wgt_accum or landings_wgt_grams
+! lpue_accum or lpue
+#ifdef ACCUM_LANDINGS
+    if (data_select%plot_LAND) then
+        call Write_Column_CSV_By_Region(num_grids, landings_accum(:), grid(1:num_grids)%lon, 'LAND', &
+        &    data_dir//'X_Y_LAND_'//domain_name//trim(buf), .true.)
+        landings_accum(:) = 0.D0
+    endif
+
+    if (data_select%plot_LNDW) then
+        call Write_Column_CSV_By_Region(num_grids, landings_wgt_accum(:), grid(1:num_grids)%lon, 'LNDW', &
+        &    data_dir//'X_Y_LNDW_'//domain_name//trim(buf), .true.)
+        landings_wgt_accum(:) = 0.D0
+    endif
+
+    if (data_select%plot_LPUE) then 
+        call Write_Column_CSV_By_Region(num_grids, lpue_accum(:), grid(1:num_grids)%lon, 'LPUE', &
+        &    data_dir//'X_Y_LPUE_'//domain_name//trim(buf), .true.)
+        lpue_accum(:) = 0.D0
+    endif
+#else
     if (data_select%plot_LAND) &
     &    call Write_Column_CSV_By_Region(num_grids, landings_by_num(:), grid(1:num_grids)%lon, 'LAND', &
     &    data_dir//'X_Y_LAND_'//domain_name//trim(buf), .true.)
@@ -890,6 +950,7 @@ subroutine Mortality_Write_At_Timestep(year, ts, state_mat, weight_grams, mortal
     if (data_select%plot_LPUE) &
     &    call Write_Column_CSV_By_Region(num_grids, lpue(:), grid(1:num_grids)%lon, 'LPUE', &
     &    data_dir//'X_Y_LPUE_'//domain_name//trim(buf), .true.)
+#endif
 
 endif ! if(mod()) = 1
 

SRC/ScallopRecruit.f90

@@ -85,6 +85,15 @@ subroutine Set_Recruitment(recruit, n_grids, dom_name, dom_area, recr_yr_strt, r
     character(fname_len) fname
     logical exists
 
+#ifdef USE_FIXED_RAND
+    ! Run with the same "random data" files to produce same results for evaluating output data
+    ! Assumes working with
+    ! * Ten years in duration, e.g. 2022 - 2031
+    ! * Recruit Yr 2012 - 2023
+    ! * HabCam Data Habcam_BySegment_2000_2011-2023 (could also pick Habcam_BySegment_2000_2011-2023_v2)
+    integer, parameter ::  rand_idx_debug(10) = (/4, 12, 8, 3, 8, 10, 12, 10, 4, 2/)
+#endif
+
     ! Used to define weighting
     !
     !       |
@@ -102,6 +111,11 @@ subroutine Set_Recruitment(recruit, n_grids, dom_name, dom_area, recr_yr_strt, r
     real(dp) sill
     integer rand_idx
 
+#ifdef USE_FIXED_RAND
+    write(*,*) term_yel, 'Recruit: Using fixed "random" index', term_blk
+#else
+    write(*,*) term_yel, 'Recruit: Using random "random" index', term_blk
+#endif
     call Read_Configuration()
     ! 
     sim_start_year = yr_start
@@ -143,7 +157,11 @@ subroutine Set_Recruitment(recruit, n_grids, dom_name, dom_area, recr_yr_strt, r
     do year = sim_start_year, sim_stop_year
         year_index = year_index + 1
 
+#ifdef USE_FIXED_RAND
+        rand_idx = rand_idx_debug(year_index)
+#else
         rand_idx = random_index()
+#endif
         random_year = recruit_yr_strt - 1 + rand_idx
 
         write(buf,'(I4)')random_year

SRC/makefile

@@ -20,7 +20,16 @@ FC = gfortran
 #-fno-automatic
 # -fcheck=all -fcheck-array-temporaries-fno-automatic -fmax-stack-var-size=100000 
 #FFLAGS = -O3  -mcmodel=medium -funroll-all-loops -ffast-math -msse -msse2 -m3dnow -m64
-FFLAGS = -g -Wall -std=f95 -fall-intrinsics 
+
+# -cpp C preprocessor that will accept macros, i.e. 
+FFLAGS = -cpp
+# #ifdef USE_FIXED_RAND uses the same vs random index for each run to show consistent output
+# #ifdef ACCUM_LANDINGS then landing values are accumulated for the year rather than just the last timestep period
+#
+FFLAGS += -DUSE_FIXED_RAND -UACCUM_LANDINGS
+# other
+FFLAGS += -g -Wall -std=f95 -fall-intrinsics 
+
 SRC_DIRS = .
 
 # Find all the f90 files we want to compile
@@ -29,7 +38,7 @@ SRCS = Globals.f90 GridManager.f90 ScallopMortality.f90 ScallopRecruit.f90 Scall
 #SRCS += $(shell find $(SRC_DIRS) -name '*.f90' | grep -v 'Globals\|DataPoint\|ScallopGrowth\|ScallopRecruit')
 SRCS += ScallopPopDensity.f90 IORoutines.f90 
 
-#LINUX, WIN?
+#LINUX, WIN? removed need for lapack and blas
 #LIBS = -L/usr/lib/x86_64-linux-gnu -llapack -lblas
 #MAC
 #LIBS = -L/usr/lib -llapack -lblas