v13c quid

bfmv5/BFMtab.xml

@@ -49,6 +49,10 @@
 <var name="R6n" maxvalue="4"    highfreq="false" dump="false" ></var>
 <var name="R6p" maxvalue="0.5"  highfreq="false" dump="false" ></var>
 <var name="R6s" maxvalue="3"    highfreq="false" dump="false" ></var>
+<var name="R8c" maxvalue="200"  highfreq="false" dump="false" ></var>
+<var name="R8n" maxvalue="4"    highfreq="false" dump="false" ></var>
+<var name="R8p" maxvalue="0.5"  highfreq="false" dump="false" ></var>
+<var name="R8s" maxvalue="3"    highfreq="false" dump="false" ></var>
 <var name="R7c" maxvalue="3000"  highfreq="false" dump="false" ></var>
 <var name="R3c" maxvalue="100000" highfreq="false" comment="max inventato" dump="false" ></var>
 <var name="O3c" maxvalue="200000" highfreq="false" dump="false" ></var>
@@ -93,6 +97,7 @@
 <var name="flN4N3n"      highfreq="false" dump="false" ></var> 
 <var name="sediR2"       highfreq="false" dump="false" ></var> 
 <var name="sediR6"       highfreq="false" dump="false" ></var> 
+<var name="sediR8"       highfreq="false" dump="false" ></var> 
 <var name="sediO5"       highfreq="false" dump="false" ></var>
 <var name="xEPS"         highfreq="false" dump="false" ></var> 
 <var name="ABIO_eps"     highfreq="false" dump="false" ></var> 
@@ -124,14 +129,17 @@
 <var name="qpcOMT_iiR2"  highfreq="false" dump="false" ></var> 
 <var name="qpcOMT_iiR3"  highfreq="false" dump="false" ></var> 
 <var name="qpcOMT_iiR6"  highfreq="false" dump="false" ></var> 
+<var name="qpcOMT_iiR8"  highfreq="false" dump="false" ></var> 
 <var name="qncOMT_iiR1"  highfreq="false" dump="false" ></var> 
 <var name="qncOMT_iiR2"  highfreq="false" dump="false" ></var> 
 <var name="qncOMT_iiR3"  highfreq="false" dump="false" ></var> 
 <var name="qncOMT_iiR6"  highfreq="false" dump="false" ></var> 
+<var name="qncOMT_iiR8"  highfreq="false" dump="false" ></var> 
 <var name="qscOMT_iiR1"  highfreq="false" dump="false" ></var> 
 <var name="qscOMT_iiR2"  highfreq="false" dump="false" ></var> 
 <var name="qscOMT_iiR3"  highfreq="false" dump="false" ></var> 
 <var name="qscOMT_iiR6"  highfreq="false" dump="false" ></var> 
+<var name="qscOMT_iiR8"  highfreq="false" dump="false" ></var> 
 <var name="qpcPBA_iiB1"  highfreq="false" dump="false" ></var> 
 <var name="qncPBA_iiB1"  highfreq="false" dump="false" ></var> 
 <var name="sediPPY_iiP1" highfreq="false" dump="false" ></var> 
@@ -218,6 +226,7 @@
 <var name="qlcOMT_iiR2"     highfreq="false" dump="false" ></var>
 <var name="qlcOMT_iiR3"     highfreq="false" dump="false" ></var>
 <var name="qlcOMT_iiR6"     highfreq="false" dump="false" ></var>
+<var name="qlcOMT_iiR8"     highfreq="false" dump="false" ></var>
 
 </Diagnostics>
 

compilers/machine_modules/g100.intel

@@ -4,17 +4,14 @@ module load intel/oneapi-2021--binary
 module load intelmpi/oneapi-2021--binary
 module load mkl/oneapi-2021--binary
 module load cmake/3.21.4
-module load netcdf/4.7.4--oneapi--2021.2.0-ifort
-module load netcdff/4.5.3--oneapi--2021.2.0-ifort
-
-# modules define these $.._HOME env variable
-export NETCDF_INC=$NETCDF_C_HOME/include
-export NETCDF_LIB=$NETCDF_C_HOME/lib
-export NETCDFF_INC=$NETCDF_FORTRAN_HOME/include
-export NETCDFF_LIB=$NETCDF_FORTRAN_HOME/lib
 
 export OPA_HOME=/g100_work/OGS23_PRACE_IT/COPERNICUS/V10C
 export OPA_HOSTNAME=g100
+
+export NETCDF_LIB=$OPA_HOME/HOST/$OPA_HOSTNAME/lib
+export NETCDF_INC=$OPA_HOME/HOST/$OPA_HOSTNAME/include
+export NETCDFF_LIB=$OPA_HOME/HOST/$OPA_HOSTNAME/lib
+export NETCDFF_INC=$OPA_HOME/HOST/$OPA_HOSTNAME/include
 export PNETCDF_LIB=$OPA_HOME/HOST/$OPA_HOSTNAME/lib
 export PNETCDF_INC=$OPA_HOME/HOST/$OPA_HOSTNAME/include
 export PETSC_LIB=$OPA_HOME/HOST/$OPA_HOSTNAME/lib

preproc/domdec/domdec_generator.py

@@ -36,9 +36,9 @@ def argument():
 max_proc_j = args.max_proc_j
 
 from domdec import *
-from commons.mask import Mask
+from bitsea.commons.mask import Mask
 
-TheMask = Mask(args.maskfile, dzvarname="e3t_0")
+TheMask = Mask.from_file(args.maskfile, e3t_var_name="e3t_0")
 tmask = TheMask.mask_at_level(0)
 jpjglo, jpiglo = tmask.shape
 

src/BC/hard_open.f90

@@ -544,7 +544,7 @@ subroutine apply_dirichlet(self)
              ! 2nd loop: provided variables on neighbors
                 do j = 1, self%m_size
 
-                    idx_i = self%m_neighbors(1, i)
+                    idx_i = self%m_neighbors(1, j)
                     idx_j = self%m_neighbors(2, j)
                     idx_k = self%m_neighbors(3, j)
 

src/BIO-OPTICS/trc3streams.f90

@@ -19,7 +19,7 @@ SUBROUTINE trc3streams(datestring)
 
 #if defined key_trc_nnpzddom || defined key_trc_npzd || key_trc_bfm
 
-      INTEGER :: jk,jj,ji,jl,bottom
+      INTEGER :: jk,jj,ji,jl,bottom, phys_bottom
       INTEGER :: day_of_year
       INTEGER :: MODE ! 0-exact, 1-approx
       INTEGER :: year, month, day, ihr
@@ -66,8 +66,8 @@ SUBROUTINE trc3streams(datestring)
              if (bfmmask(1,jj,ji) == 0) CYCLE
 
 
-             bottom = mbathy(jj,ji)
-             bottom = min(bottom,jpk_opt) ! Stop at approx 500 mt
+             phys_bottom = mbathy(jj,ji)
+             bottom = min(phys_bottom,jpk_opt) ! Stop at approx 500 mt
 
              allocate( E(3,bottom+1,nlt))
              allocate( PARz(bottom,nchl+1))
@@ -164,12 +164,27 @@ SUBROUTINE trc3streams(datestring)
                         Eu(jk,jj,ji,jl) = E(3,jk,jl)
 
                     enddo
+
+                    if ((bottom+1).lt.phys_bottom) then
+
+                       do jk=bottom+1, phys_bottom ! propagation 500m --> phys_bottom of last value
+                          Ed(jk,jj,ji,jl) = Ed(bottom+1, jj,ji, jl)
+                          Es(jk,jj,ji,jl) = Es(bottom+1, jj,ji, jl)
+                          Eu(jk,jj,ji,jl) = Eu(bottom+1, jj,ji, jl)
+                       enddo
+                    endif
                  enddo
 
                  do jl=1, nchl+1
                     do jk =1, bottom
                         PAR(jk,jj,ji,jl) = PARz(jk,jl)
                     enddo
+                    if (bottom.lt.phys_bottom) then
+                        do jk=bottom+1, phys_bottom ! propagation of last value
+                          PAR(jk,jj,ji,jl) = PARz(bottom,jl)
+                        enddo
+                    endif
+
                  enddo 
 
 

src/BIO/SED_mem.f90

@@ -16,7 +16,7 @@ MODULE SED_mem
 
 
       INTEGER :: dimen_jvsed
-      INTEGER :: nsed=22
+      INTEGER :: nsed=26
       INTEGER, allocatable :: sed_idx(:)
       INTEGER, allocatable :: jarr_sed(:,:),jarr_sed_flx(:,:)
       double precision, allocatable :: ztra(:,:)
@@ -54,27 +54,32 @@ subroutine myalloc_SED()
        sed_idx(3)  = ppR6p
        sed_idx(4)  = ppR6s
 
-       sed_idx(5)  = ppP1c
-       sed_idx(6)  = ppP1n
-       sed_idx(7)  = ppP1p
-       sed_idx(8)  = ppP1s
-       sed_idx(9)  = ppP1l
-
-       sed_idx(10) = ppP2c
-       sed_idx(11) = ppP2n
-       sed_idx(12) = ppP2p
-       sed_idx(13) = ppP2l
-
-       sed_idx(14) = ppP3c
-       sed_idx(15) = ppP3n
-       sed_idx(16) = ppP3p
-       sed_idx(17) = ppP3l
-
-       sed_idx(18) = ppP4c
-       sed_idx(19) = ppP4n
-       sed_idx(20) = ppP4p
-       sed_idx(21) = ppP4l
-       sed_idx(22) = ppO5c
+       sed_idx(5)  = ppR8c
+       sed_idx(6)  = ppR8n
+       sed_idx(7)  = ppR8p
+       sed_idx(8)  = ppR8s
+
+       sed_idx(9)  = ppP1c
+       sed_idx(10)  = ppP1n
+       sed_idx(11)  = ppP1p
+       sed_idx(12)  = ppP1s
+       sed_idx(13)  = ppP1l
+
+       sed_idx(14) = ppP2c
+       sed_idx(15) = ppP2n
+       sed_idx(16) = ppP2p
+       sed_idx(17) = ppP2l
+
+       sed_idx(18) = ppP3c
+       sed_idx(19) = ppP3n
+       sed_idx(20) = ppP3p
+       sed_idx(21) = ppP3l
+
+       sed_idx(22) = ppP4c
+       sed_idx(23) = ppP4n
+       sed_idx(24) = ppP4p
+       sed_idx(25) = ppP4l
+       sed_idx(26) = ppO5c
        allocate(jarr_sed(2, jpi*jpj))        
        jarr_sed     = huge(jarr_sed(1,1))
        allocate(jarr_sed_flx(jpk,jpi*jpj)) 

src/BIO/trcsed.f90

@@ -133,39 +133,45 @@ SUBROUTINE trcsed
 
 
 
-!                Particulate
+!              Small Particulate
               DO js =1,4
                  DO  jk = 2,jpkm1
-                    zwork(jk,js,1) = -vsed * trn(jk-1,jj,ji, sed_idx(js))
+                    zwork(jk,js,1) = -vsedR6 * trn(jk-1,jj,ji, sed_idx(js))
+                 END DO
+              END DO
+!              Large Particulate
+              DO js =5,8
+                 DO  jk = 2,jpkm1
+                    zwork(jk,js,1) = -vsedR8 * trn(jk-1,jj,ji, sed_idx(js))
                  END DO
               END DO
 !                Diatoms
-              DO js =5,9
+              DO js =9,13
                  DO  jk = 2,jpkm1
                     zwork(jk,js,1) = -ogstm_sedipi(jk-1,jj,ji,1) * trn(jk-1,jj,ji, sed_idx(js))
                  END DO
               END DO
 !                Flagellates
-              DO js =10,13
+              DO js =14,17
                  DO  jk = 2,jpkm1
                     zwork(jk,js,1) = -ogstm_sedipi(jk-1,jj,ji,2) * trn(jk-1,jj,ji, sed_idx(js))
                  END DO
               END DO
 !                Picophytoplankton
-              DO js =14,17
+              DO js =18,21
                  DO  jk = 2,jpkm1
                     zwork(jk,js,1) = -ogstm_sedipi(jk-1,jj,ji,3) * trn(jk-1,jj,ji, sed_idx(js))
                  END DO
               END DO
 !                Dinoflagellates
-              DO js =18,21
+              DO js =22,25
                  DO  jk = 2,jpkm1
                     zwork(jk,js,1) = -ogstm_sedipi(jk-1,jj,ji,4) * trn(jk-1,jj,ji, sed_idx(js))
                  END DO
               END DO
 
 !                Calcite
-              DO js =22,22
+              DO js =26,26
                  DO  jk = 2,jpkm1
                     zwork(jk,js,1) = - vsedO5c * trn(jk-1,jj,ji, sed_idx(js))
                  END DO

src/DA/external_scripts/float_postproc/makeplots_postDA.py

@@ -10,7 +10,7 @@
 
 
 def plot_floatvsmodel(modelvarname,idate1,AllProfiles,AllChl, NewPres, Float,wmolist):
-        TheMask=Mask("/pico/home/usera07ogs/a07ogs00/OPA/V2C/etc/static-data/MED1672_cut/MASK/meshmask.nc")
+        TheMask=Mask.from_file("/pico/home/usera07ogs/a07ogs00/OPA/V2C/etc/static-data/MED1672_cut/MASK/meshmask.nc")
         nav_lev = TheMask.zlevels
         dz= TheMask.dz
 

src/DA/external_scripts/float_postproc/postproc_float_3dvar.py

@@ -74,7 +74,7 @@ def argument():
 read_adjusted = [True] #,False,False]
 
 # MASK of the domain
-TheMask=Mask("/pico/home/usera07ogs/a07ogs00/OPA/V2C/etc/static-data/MED1672_cut/MASK/meshmask.nc")
+TheMask=Mask.from_file("/pico/home/usera07ogs/a07ogs00/OPA/V2C/etc/static-data/MED1672_cut/MASK/meshmask.nc")
 nav_lev = TheMask.zlevels
 
 layer=Layer(0,200)     #layer of the Float profile???? 

src/DA/external_scripts/float_postproc/var_aggregator.py

@@ -92,7 +92,7 @@ def addsep(string):
 
 SingleVar_filelist=glob.glob(PATH_NAME)
 SingleVar_filelist.sort()
-TheMask=Mask(args.maskfile)
+TheMask=Mask.from_file(args.maskfile)
 
 for N1pfile in SingleVar_filelist[rank::nranks]:
     dailyAve  = os.path.basename(N1pfile)

src/DA/external_scripts/float_preproc/CheckFloatperDate.py

@@ -73,7 +73,7 @@ def argument():
 read_adjusted = [True] #,False,False]
 
 # MASK of the domain
-TheMask=Mask("/pico/home/usera07ogs/a07ogs00/OPA/V2C/etc/static-data/MED1672_cut/MASK/meshmask.nc")
+TheMask=Mask.from_file("/pico/home/usera07ogs/a07ogs00/OPA/V2C/etc/static-data/MED1672_cut/MASK/meshmask.nc")
 nav_lev = TheMask.zlevels
 
 layer=Layer(0,200)     #layer of the Float profile???? 

src/DA/external_scripts/float_preproc/CheckFloatperDate_calcalastd.py

@@ -72,7 +72,7 @@ def argument():
 read_adjusted = [True] #,False,False]
 
 # MASK of the domain
-TheMask=Mask("/pico/home/usera07ogs/a07ogs00/OPA/V2C/etc/static-data/MED1672_cut/MASK/meshmask.nc")
+TheMask=Mask.from_file("/pico/home/usera07ogs/a07ogs00/OPA/V2C/etc/static-data/MED1672_cut/MASK/meshmask.nc")
 nav_lev = TheMask.zlevels
 
 layer=Layer(0,200)     #layer of the Float profile???? 

src/DA/external_scripts/float_preproc/Float_misfit_gen.sh

@@ -25,7 +25,7 @@ echo "Float_misfit_gen.sh start "
 source ${OPA_SCRDIR}/opa_profile.inc
 #opa_prex "module unload numpy"
 opa_prex "source $OPA_VENV_1/bin/activate"
-export PYTHONPATH=${PYTHONPATH}:$OPA_BITSEA
+export PYTHONPATH=$OPA_BITSEA:${PYTHONPATH}
 
 while [ True ] ; do
   while [ True ] ; do

src/DA/external_scripts/float_preproc/float_extractor.py

@@ -38,15 +38,15 @@ def argument():
 
 args = argument()
 
-from commons.time_interval import TimeInterval
-from commons.Timelist import TimeList
-from instruments.matchup_manager import Matchup_Manager
-import basins.OGS as OGS
-from instruments.var_conversions import FLOATVARS
-from commons.utils import addsep
+from bitsea.commons.time_interval import TimeInterval
+from bitsea.commons.Timelist import TimeList
+from bitsea.instruments.matchup_manager import Matchup_Manager
+import bitsea.basins.OGS as OGS
+from bitsea.instruments.var_conversions import FLOATVARS
+from bitsea.commons.utils import addsep
 from datetime import timedelta
 from datetime import datetime
-from commons import timerequestors
+from bitsea.commons import timerequestors
 import numpy as np
 import os,sys
 
@@ -56,9 +56,9 @@ def argument():
     sys.exit(1)
 assert profilesource in ["superfloat", "ppcon"]
 if profilesource=="superfloat":
-    from instruments import superfloat as bio_float
+    from bitsea.instruments import superfloat as bio_float
 if profilesource=="ppcon":
-    from instruments import float_ppcon as bio_float
+    from bitsea.instruments import float_ppcon as bio_float
 
 
 meantime=datetime.strptime(args.time,'%Y%m%d')