Neccton

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 +4,22 @@ 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
+#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=$NETCDF_FORTRAN_HOME/lib
+#export NETCDF_INC=$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.py

@@ -1,5 +1,5 @@
 import numpy as np
-import pylab as pl
+#import pylab as pl
 
 def riparto(lenglo,nprocs):
     ''' Uniform decomposition of a 1d array of size lenglo in nprocs subdomains
@@ -212,51 +212,51 @@ def neighbors(M,nproc,nproci,nprocj):
 
 
 
-def plot_decomposition(tmask, nproci, nprocj):
-    '''
-    Plots the domain decomposition scheme
-
-    Arguments :
-    * tmask  * a 2d logical array, the surface tmask
-    * nproci * integer, number of longitudinal subdivisions
-    * nprocj * integer, number of latitudinal subdivisions
-
-    Returns:
-    fig, ax : matplotlib handles
-    '''
-    jpjglo, jpiglo = tmask.shape
-    M,C = get_wp_matrix(tmask, nprocj, nproci)
-    J,I = M.nonzero()
-    nproc = len(I)
-
-    JPI = riparto(jpiglo,nproci)
-    Start_I = get_startpoints(JPI)
-    End_I = Start_I + JPI -1
-
-    JPJ = riparto(jpjglo,nprocj)
-    Start_J = get_startpoints(JPJ)
-    End_J = Start_J + JPJ -1
-
-    fig,ax = pl.subplots()
-    ax.imshow(tmask)
-    for i in range(1,nproci):
-        x=Start_I[i]
-        ax.plot([x,x],[0,jpjglo],'w')
-
-    for j in range(1,nprocj):
-        y=Start_J[j]
-        ax.plot([0,jpiglo],[y,y],'w')
-
-    for rank in range(nproc):
-        j = J[rank]
-        i = I[rank]
-        x = Start_I[i] + JPI[0]/2
-        y = Start_J[j] + JPJ[0]/2
-        ax.text(x,y,str(rank), color='w', ha='center', va='center', fontsize=8)
-
-
-    ax.invert_yaxis()
-    return fig, ax
+#def plot_decomposition(tmask, nproci, nprocj):
+#    '''
+#    Plots the domain decomposition scheme
+#
+#    Arguments :
+#    * tmask  * a 2d logical array, the surface tmask
+#    * nproci * integer, number of longitudinal subdivisions
+#    * nprocj * integer, number of latitudinal subdivisions
+#
+#    Returns:
+#    fig, ax : matplotlib handles
+#    '''
+#    jpjglo, jpiglo = tmask.shape
+#    M,C = get_wp_matrix(tmask, nprocj, nproci)
+#    J,I = M.nonzero()
+#    nproc = len(I)
+#
+#    JPI = riparto(jpiglo,nproci)
+#    Start_I = get_startpoints(JPI)
+#    End_I = Start_I + JPI -1
+#     
+#    JPJ = riparto(jpjglo,nprocj)
+#    Start_J = get_startpoints(JPJ)
+#    End_J = Start_J + JPJ -1
+#    
+#    fig,ax = pl.subplots()
+#    ax.imshow(tmask)
+#    for i in range(1,nproci):
+#        x=Start_I[i]
+#        ax.plot([x,x],[0,jpjglo],'w')
+#    
+#    for j in range(1,nprocj):
+#        y=Start_J[j]
+#        ax.plot([0,jpiglo],[y,y],'w')
+#    
+#    for rank in range(nproc):
+#        j = J[rank]
+#        i = I[rank]
+#        x = Start_I[i] + JPI[0]/2
+#        y = Start_J[j] + JPJ[0]/2
+#        ax.text(x,y,str(rank), color='w', ha='center', va='center', fontsize=8)
+#    
+#    
+#    ax.invert_yaxis()
+#    return fig, ax
 
 
 

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+1 ! 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

@@ -133,40 +133,46 @@ 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))
+                 DO  jk = 2,jpk
+                    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,jpk
+                    zwork(jk,js,1) = -vsedR8 * trn(jk-1,jj,ji, sed_idx(js))
                  END DO
               END DO
 !                Diatoms
-              DO js =5,9
-                 DO  jk = 2,jpkm1
+              DO js =9,13
+                 DO  jk = 2,jpk
                     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  jk = 2,jpkm1
+              DO js =14,17
+                 DO  jk = 2,jpk
                     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  jk = 2,jpkm1
+              DO js =18,21
+                 DO  jk = 2,jpk
                     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  jk = 2,jpkm1
+              DO js =22,25
+                 DO  jk = 2,jpk
                     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  jk = 2,jpkm1
+              DO js =26,26
+                 DO  jk = 2,jpk
                     zwork(jk,js,1) = - vsedO5c * trn(jk-1,jj,ji, sed_idx(js))
                  END DO
               END DO
@@ -175,11 +181,23 @@ SUBROUTINE trcsed
 
 ! 1.3 tracer flux divergence at t-point added to the general trend
 
+!N            DO js =1,nsed
+!N                if ((ji .EQ. 3) .AND. (jj .EQ. 3 )) then
+!N                    write(*,*) ' Check trcsed'
+!N                    write(*,*)'Sedimenting variable',js
+!N                    write(*,*)'e3t',e3t(jpk,jj,ji), e3t(jpk-1,jj,ji), e3t(jpk-2,jj,ji) 
+!N                    write(*,*)'zwork at above above bottom:', zwork(jpk-2,js,1)
+!N                    write(*,*)'zwork at above bottom:', zwork(jpk-1,js,1)
+!N                    write(*,*)'zwork at bottom:', zwork(jpk,js,1)
+!N                    write(*,*) ' ******************* '
+!N                 endif
+!N            ENDDO
+
               DO  jk = 1,jpkm1
                   jf=  jarr_sed_flx(jk,jV)
 
                  ze3tr = 1./e3t(jk,jj,ji)
-
+ 
                  DO js =1,nsed
                     ztra(js,1) = -ze3tr * (zwork(jk,js,1) - zwork(jk+1,js,1))
                     IF ((Fsize .GT. 0) .AND. (jf .GT. 0)) THEN
@@ -191,6 +209,10 @@ SUBROUTINE trcsed
 !!!  d2s convert speed from (m/day) to  (m/s)
                     tra(jk,jj,ji,sed_idx(js)) = tra(jk,jj,ji,sed_idx(js)) + ztra(js,1)*d2s
                  END DO
+!N             if ((ji .EQ. 3) .AND. (jj .EQ. 3 )) then
+!N                 if (jk .EQ.  jpk-1) write(*,*) 'R6c at bottom:', tra(jk,jj,ji,sed_idx(1))
+!N                 if (jk .EQ.  jpk-1) write(*,*) 'ztra at bottom:', ztra(1,1)
+!N             endif
 
 #ifdef key_trc_diabio
                   trbio(jk,jj,ji,8) = ztra

src/General/memory.f90

@@ -391,7 +391,8 @@ MODULE myalloc
       LOGICAL atlantic_bfm ! atlantic buffer biology activation
 
 #    if defined key_trc_bfm
-      double precision vsed                        ! sedimentation speed (NAMELIST)
+      double precision vsedR6                      ! sedimentation speed of small detritus (NAMELIST)
+      double precision vsedR8                      ! sedimentation speed of large detritus (NAMELIST)
       double precision vsedO5c                     ! sedimentation speed of calcite(NAMELIST)
       double precision bottom_flux                 ! (NAMELIST)