Offline sediment spinup

cime_config/buildcpp

@@ -74,6 +74,7 @@ def buildcpp(case):
     ocn_grid = case.get_value("OCN_GRID")
     turbclo = case.get_value("BLOM_TURBULENT_CLOSURE")
     tracers = case.get_value("BLOM_TRACER_MODULES")
+    sed_spinoff = case.get_value("HAMOCC_OFFLINE_SEDIMENT_SPINUP")
     blom_atrc = case.get_value("BLOM_ATRC")
     pio_typename = case.get_value("PIO_TYPENAME", subgroup="OCN")
 
@@ -118,6 +119,8 @@ def buildcpp(case):
                 blom_cppdefs = blom_cppdefs + " -DHAMOCC"
             else:
                 expect(False, "tracer module {} is not recognized".format(module))
+        if sed_spinoff:
+          blom_cppdefs = blom_cppdefs + " -DOFFLINE_SEDIMENT_SPINUP"
 
     if blom_atrc:
         blom_cppdefs = blom_cppdefs + " -DATRC"

cime_config/config_component.xml

@@ -277,6 +277,18 @@
     <desc>Set namelist option to activate the carbon isotope code. Requires module ecosys</desc>
   </entry>
 
+  <entry id="HAMOCC_OFFLINE_SEDIMENT_SPINUP">
+    <type>logical</type>
+    <valid_values>TRUE,FALSE</valid_values>
+    <default_value>FALSE</default_value>
+    <values>
+      <value compset="_BLOM.*%ECO">FALSE</value>
+    </values>
+    <group>build_component_blom</group>
+    <file>env_build.xml</file>
+    <desc>Offline sediment spinup. Requires module ecosys</desc>
+  </entry>
+
   <entry id="HAMOCC_SEDBYPASS">
     <type>logical</type>
     <valid_values>TRUE,FALSE</valid_values>

cime_config/config_compsets.xml

@@ -123,7 +123,7 @@
 
 
   <!-- JRA repeat year forcing - no prognostic wave -->
-  
+
   <compset>
     <alias>NOINYJRARYF1961OC</alias>
     <lname>1850_DATM%JRARYF1961_SLND_CICE_BLOM%HYB%ECO_DROF%JRARYF1961_SGLC_SWAV</lname>
@@ -142,14 +142,32 @@
     <lname>1850_DATM%JRA-RYF8485_SLND_CICE_BLOM%HYB%ECO_DROF%JRA-RYF8485_SGLC_SWAV</lname>
   </compset>
 
-  
+
   <!-- CPLHIST forcing - no prognostic wave -->
 
   <compset>
     <alias>NOICPLHISTOC</alias>
     <lname>1850_DATM%CPLHIST_SLND_CICE_BLOM%HYB%ECO_DROF%CPLHIST_SGLC_SWAV</lname>
   </compset>
 
+  <!-- Offline sediment spinup -->
+
+  <!--<compset> EXAMPLE FROM CAM
+    <alias>FADIAB</alias>
+    <lname>2000_CAM%ADIAB_SLND_SICE_SOCN_SROF_SGLC_SWAV</lname>
+  </compset>-->
+
+  <compset>
+    <!-- offline sediment spinup for hybrid coordinates -->
+    <alias>OFFLSEDH</alias>
+    <lname>SCAM_SLND_SICE_BLOM%HYB%ECO_SROF_SGLC_SWAV</lname>
+  </compset>
+  <compset>
+    <!-- offline sediment spinup for hybrid coordinates -->
+    <alias>OFFLSED</alias>
+    <lname>SCAM_SLND_SICE_BLOM%ECO_SROF_SGLC_SWAV</lname>
+  </compset>
+
   <entries>
     <entry id="RUN_STARTDATE">
       <values match="last">

cime_config/config_pes.xml

@@ -1019,5 +1019,43 @@
     </mach>
   </grid>
 
+  <!-- Offline sediment spinup - testwise - needs adjustment to reduce idling -->
+  <grid name="a%null.+oi%tnx2v1">
+    <mach name="any">
+      <pes pesize="M" compset="SCAM.*_BLOM.*%ECO">
+        <comment>Medium sized pe-layout with 384 pes in total</comment>
+        <ntasks>
+          <ntasks_atm>18</ntasks_atm>
+          <ntasks_rof>18</ntasks_rof>
+          <ntasks_ice>76</ntasks_ice>
+          <ntasks_ocn>272</ntasks_ocn>
+          <ntasks_cpl>76</ntasks_cpl>
+          <ntasks_lnd>1</ntasks_lnd>
+          <ntasks_glc>1</ntasks_glc>
+          <ntasks_wav>1</ntasks_wav>
+        </ntasks>
+        <nthrds>
+          <nthrds_atm>1</nthrds_atm>
+          <nthrds_lnd>1</nthrds_lnd>
+          <nthrds_rof>1</nthrds_rof>
+          <nthrds_ice>1</nthrds_ice>
+          <nthrds_ocn>1</nthrds_ocn>
+          <nthrds_glc>1</nthrds_glc>
+          <nthrds_wav>1</nthrds_wav>
+          <nthrds_cpl>1</nthrds_cpl>
+        </nthrds>
+        <rootpe>
+          <rootpe_atm>76</rootpe_atm>
+          <rootpe_lnd>0</rootpe_lnd>
+          <rootpe_rof>94</rootpe_rof>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_ocn>112</rootpe_ocn>
+          <rootpe_glc>0</rootpe_glc>
+          <rootpe_wav>0</rootpe_wav>
+          <rootpe_cpl>0</rootpe_cpl>
+        </rootpe>
+      </pes>
+    </mach>
+  </grid>
 
 </config_pes>

cime_config/namelist_definition_blom.xml

@@ -4603,6 +4603,18 @@
     </desc>
   </entry>
 
+  <entry id="sedspinoff_file" is_inputdata="yes">
+    <type>char</type>
+    <category>bgcnml</category>
+    <group>bgcnml</group>
+    <values>
+      <value>''</value>
+    </values>
+    <desc>
+      File name (incl. full path) for offline sediment spinup - holding climatological mean of carflx_bot,calflx_bot,dustflx_bot and bsiflx_bot
+    </desc>
+  </entry>
+
   <entry id="shelfsea_maskfile" is_inputdata="yes">
     <type>char</type>
     <category>bgcnml</category>

drivers/nuopc/ocn_comp_nuopc.F90

@@ -99,6 +99,9 @@ module ocn_comp_nuopc
 
    public :: SetServices, SetVM
 
+   logical :: mediator_present ! jm enabling to switch of mediator and data provision for sediment offline spinup
+                               ! see eg.: https://github.com/NorESMhub/CAM/blob/cda829d695a6cc8c14f56b89f4a86830c9b919a9/src/cpl/nuopc/atm_comp_nuopc.F90
+
 !================================================================================
 contains
 !================================================================================
@@ -371,6 +374,9 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
    ! The NUOPC layer uses these to match fields between components in the
    ! coupled system.
    ! ---------------------------------------------------------------------------
+!jm offline sediment spinup
+      use shr_sys_mod         , only : shr_sys_abort
+!jm end offline sediment spinup
 
       ! Input/output arguments.
       type(ESMF_GridComp)  :: gcomp
@@ -407,6 +413,22 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
       use_BROMO = .false.
 #endif
 
+!jm offline sediment spinup
+      ! Get info if mediator is present
+      call NUOPC_CompAttributeGet(gcomp, name="mediator_present", value=cvalue, &
+                                  isPresent=isPresent, isSet=isSet, rc=rc)
+      if (ChkErr(rc,__LINE__,u_FILE_u)) return
+      if (isPresent .and. isSet) then
+        read (cvalue,*) mediator_present
+!        if (mediator_present) then
+!          call advertise_fields(gcomp, flds_scalar_name, rc)
+!          if (ChkErr(rc,__LINE__,u_FILE_u)) return
+!        end if
+      else
+       call shr_sys_abort(subname//'Need to set attribute mediator_present')
+      endif
+!jm end offline sediment spinup
+
       ! Get debug flag.
       call NUOPC_CompAttributeGet(gcomp, name='dbug_flag', value=cvalue, &
                                   isPresent=isPresent, isSet=isSet, rc=rc)
@@ -612,6 +634,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
 
 
 
+if (mediator_present) then !jm offline-sediment-spinup
       ! ------------------------------------------------------------------------
       ! Advertise import fields.
       ! ------------------------------------------------------------------------
@@ -637,6 +660,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
                               TransferOfferGeomObject='will provide', rc=rc)
          if (ChkErr(rc, __LINE__, u_FILE_u)) return
       enddo
+endif ! mediator_present jm offline-sediment-spinup
 
       if (dbug > 5) call ESMF_LogWrite(subname//': done', ESMF_LOGMSG_INFO)
 
@@ -730,6 +754,8 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
 
       call blom_setareacor(areaMesh, maskMesh)
 
+! jm offline sediment spinup
+if (mediator_present) then
       ! ------------------------------------------------------------------------
       ! Realize the actively coupled fields.
       ! ------------------------------------------------------------------------
@@ -771,6 +797,8 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
          call ocn_stream_sst_init(Emesh, clock, rc)
          if (ChkErr(rc, __LINE__, u_FILE_u)) return
       end if
+! jm offline sediment spinup
+endif
 
       ! Find if restart is needed at the end of the run
       call NUOPC_CompAttributeGet(gcomp, name="write_restart_at_endofrun", value=cvalue, isPresent=isPresent, isSet=isSet, rc=rc)
@@ -780,11 +808,15 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
       end if
 
 #ifdef HAMOCC
+! jm offline sediment spinup
+if (mediator_present) then
       ! Initialize sdat for dust deposition climatology if appropriate
       if (use_stream_dust) then
          call ocn_stream_dust_init(Emesh, clock, rc)
          if (ChkErr(rc, __LINE__, u_FILE_u)) return
       end if
+! jm offline sediment spinup
+endif
 #endif
 
       if (dbug > 5) call ESMF_LogWrite(subname//': done', ESMF_LOGMSG_INFO)
@@ -838,6 +870,8 @@ subroutine DataInitialize(gcomp, rc)
 
       call timer_stop('initialization', &
                       'between blom_init_phase1 and blom_init_phase2')
+! jm offline sediment spinup
+if (mediator_present) then
       call blom_init_phase2
       call timer_stop('initialization', 'blom_init_phase2')
 
@@ -871,6 +905,8 @@ subroutine DataInitialize(gcomp, rc)
          call ESMF_LogWrite("BLOM - Initialize-Data-Dependency NOT SATISFIED!!!", &
                             ESMF_LOGMSG_INFO)
       endif
+! jm offline sediment spinup
+endif
 
       if (dbug > 5) call ESMF_LogWrite(subname//': done', ESMF_LOGMSG_INFO)
 

hamocc/meson.build

@@ -36,7 +36,9 @@ sources += files(
   'mo_read_oafx.F90',
   'mo_read_sedpor.F90',
   'mo_read_sedqual.F90',
+  'mo_read_sedspinoff.F90',
   'mo_sedmnt.F90',
+  'mo_sedmnt_spinoff.F90',
   'mo_vgrid.F90',
   'mo_ncout_hamocc.F90',
   'mo_netcdf_bgcrw.F90',

hamocc/mo_carchm.F90

@@ -25,7 +25,7 @@ module mo_carchm
   private
 
   public  :: carchm
-  public  :: carchm_solve
+  public  :: carchm_solve, carchm_kequi
 
   ! Maximum number of iterations for carbon chemistry solver
   integer, parameter :: niter=20

hamocc/mo_control_bgc.F90

@@ -95,6 +95,12 @@ module mo_control_bgc
   logical           :: use_river2omip         = .false. ! River2ocean MIP protocol
   logical           :: use_DOMclasses         = .false. ! DOM classes (labile, semi-labile,semi-refractory and refractory)
 
+#ifdef OFFLINE_SEDIMENT_SPINUP
+  logical           :: offline_sediment_spinup = .true.
+#else
+  logical           :: offline_sediment_spinup = .false.
+#endif
+
 contains
 
   subroutine get_bgc_namelist

hamocc/mo_hamocc_init.F90

@@ -48,7 +48,7 @@ subroutine hamocc_init(read_rest,rstfnm_hamocc)
                               lkwrbioz_off,do_n2o_coupled,do_nh3_coupled,                          &
                               ocn_co2_type, use_sedbypass, use_BOXATM, use_BROMO,use_extNcycle,    &
                               use_coupler_ndep,lTO2depremin,use_sediment_quality,ldyn_sed_age,     &
-                              linit_DOMclasses_sim
+                              linit_DOMclasses_sim,offline_sediment_spinup
     use mo_param1_bgc,  only: ks,init_por2octra_mapping
     use mo_param_bgc,   only: ini_parambgc,claydens,calcdens,calcwei,opaldens,opalwei,ropal,       &
                             & ini_bgctimes,sec_per_day
@@ -65,6 +65,7 @@ subroutine hamocc_init(read_rest,rstfnm_hamocc)
     use mo_read_pi_ph,  only: ini_pi_ph,pi_ph_file
     use mo_read_sedpor, only: read_sedpor,sedporfile,sed_por
     use mo_read_sedqual,only: read_sedqual,sedqualfile, sed_POCage_init,prorca_mavg_init
+    use mo_read_sedspinoff,only: read_sedspinoff,sedspinoff_file
     use mo_clim_swa,    only: ini_swa_clim,swaclimfile
     use mo_Gdata_read,  only: inidic,inialk,inipo4,inioxy,inino3,inisil,inid13c,inid14c,inidom
     use mo_intfcblom,   only: alloc_mem_intfcblom,nphys,bgc_dx,bgc_dy,bgc_dp,bgc_rho,omask,        &
@@ -90,7 +91,7 @@ subroutine hamocc_init(read_rest,rstfnm_hamocc)
          &            inidic,inialk,inipo4,inioxy,inino3,inisil,inid13c,inid14c,inidom,swaclimfile,&
          &            with_dmsph,pi_ph_file,l_3Dvarsedpor,sedporfile,ocn_co2_type,                 &
          &            do_n2o_coupled,do_nh3_coupled,lkwrbioz_off,lTO2depremin,shelfsea_maskfile,   &
-         &            sedqualfile,ldyn_sed_age,linit_DOMclasses_sim,dzs,sed_porosity
+         &            sedqualfile,ldyn_sed_age,linit_DOMclasses_sim,dzs,sed_porosity,sedspinoff_file
     !
     ! --- Set io units and some control parameters
     !
@@ -113,6 +114,13 @@ subroutine hamocc_init(read_rest,rstfnm_hamocc)
       write(io_stdo_bgc,*) 'date',date
       write(io_stdo_bgc,*) 'time step',dtbgc
       write(io_stdo_bgc,*) 'nday_in_year ',nday_in_year
+      if (offline_sediment_spinup) then
+        write(io_stdo_bgc,*) '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!'
+        write(io_stdo_bgc,*) ' '
+        write(io_stdo_bgc,*) 'Performing offline sediment spinup - NO WATER COLUMN BGC!!!!'
+        write(io_stdo_bgc,*) ' '
+        write(io_stdo_bgc,*) '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!'
+      endif
     endif
 
     !
@@ -209,6 +217,9 @@ subroutine hamocc_init(read_rest,rstfnm_hamocc)
     call read_sedpor(idm,jdm,ks,omask)
     !     Second, read the sediment POC age and climatological prorca and pot. apply it in ini_sedmnt
     call read_sedqual(idm,jdm,ks,omask)
+    !     Third, potentially read climatology for offline sediment spinup
+    call read_sedspinoff(idm,jdm,omask)
+    !     Eventually, initialize the sediment
     call ini_sedmnt(idm,jdm,omask,sed_por,sed_POCage_init,prorca_mavg_init)
 
     !