Making preformed tracers optional to enable HR runs without them (#394)

* Making preformed tracers optional to enable HR runs without them Run with preformed tracers enabled by default
NorESMhub · Sep 10, 2024 · 96089fa · 96089fa
1 parent 53b8173
commit 96089fa
Show file tree

Hide file tree

Showing 11 changed files with 287 additions and 215 deletions.
diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -31,7 +31,7 @@
     <default_value>FALSE</default_value>
     <group>build_component_blom</group>
     <file>env_build.xml</file>
-    <desc>Set preprocessor option to activate age tracer code. Requires module iage or ecosys</desc>
+    <desc>Set namelist option to activate age tracer code. Requires module iage or ecosys</desc>
   </entry>
 
   <entry id="BLOM_TURBULENT_CLOSURE">
@@ -148,12 +148,12 @@
        <value compset="_BGC.*%N2OC">TRUE</value>
        <value compset="_BGC.*%NH3C">TRUE</value>
        <value compset="_BGC.*%ATMNDEPC">TRUE</value>
-    </values>	    
+    </values>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
-    <desc>Set preprocessor option to activate the extended nitrogen cycle code. Requires module ecosys</desc>
+    <desc>Set namelist option to activate the extended nitrogen cycle code. Requires module ecosys</desc>
   </entry>
-  
+
   <entry id="HAMOCC_ATMNDEPC">
     <type>logical</type>
     <valid_values>TRUE,FALSE</valid_values>
@@ -165,7 +165,7 @@
     <file>env_run.xml</file>
     <desc>Nitrogen deposition coupled from atmosphere. Requires module ecosys and extncycle</desc>
   </entry>
-  
+
   <entry id="HAMOCC_N2OC">
     <type>logical</type>
     <valid_values>TRUE,FALSE</valid_values>
@@ -184,7 +184,16 @@
     <default_value>FALSE</default_value>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
-    <desc>Set preprocessor option to activate the M4AGO sinking scheme. Requires module ecosys</desc>
+    <desc>Set namelist option to activate the M4AGO sinking scheme. Requires module ecosys</desc>
+  </entry>
+
+  <entry id="HAMOCC_PREF_TRACERS">
+    <type>logical</type>
+    <valid_values>TRUE,FALSE</valid_values>
+    <default_value>TRUE</default_value>
+    <group>run_component_blom</group>
+    <file>env_run.xml</file>
+    <desc>Set namelist option to activate the preformed tracer code. Requires module ecosys</desc>
   </entry>
 
   <entry id="HAMOCC_CISO">
@@ -193,7 +202,7 @@
     <default_value>FALSE</default_value>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
-    <desc>Set preprocessor option to activate the carbon isotope code. Requires module ecosys</desc>
+    <desc>Set namelist option to activate the carbon isotope code. Requires module ecosys</desc>
   </entry>
 
   <entry id="HAMOCC_SEDBYPASS">
@@ -202,7 +211,7 @@
     <default_value>FALSE</default_value>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
-    <desc>Set preprocessor option to bypass the sediment code. Requires module ecosys</desc>
+    <desc>Set namelist option to bypass the sediment code. Requires module ecosys</desc>
   </entry>
 
   <entry id="HAMOCC_SEDSPINUP">
@@ -211,7 +220,7 @@
     <default_value>TRUE</default_value>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
-    <desc>Activate sediment spinup. HAMOCC_SEDSPINUP_YR_START and HAMOCC_SEDSPINUP_YR_END 
+    <desc>Activate sediment spinup. HAMOCC_SEDSPINUP_YR_START and HAMOCC_SEDSPINUP_YR_END
       need to be set to valid values for this option to take effect. Requires module ecosys</desc>
   </entry>
 
@@ -221,7 +230,7 @@
     <default_value>1</default_value>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
-    <desc>Set start year for HAMOCC sediment spin-up if HAMOCC_SEDSPINUP == TRUE. 
+    <desc>Set start year for HAMOCC sediment spin-up if HAMOCC_SEDSPINUP == TRUE.
       Requires module ecosys</desc>
   </entry>
 
@@ -231,17 +240,17 @@
     <default_value>800</default_value>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
-    <desc>Set end year for HAMOCC sediment spin-up if HAMOCC_SEDSPINUP == TRUE. 
+    <desc>Set end year for HAMOCC sediment spin-up if HAMOCC_SEDSPINUP == TRUE.
       Requires module ecosys</desc>
   </entry>
- 
+
   <entry id="HAMOCC_SEDSPINUP_NCYCLE">
     <type>integer</type>
     <valid_values/>
     <default_value>20</default_value>
     <group>run_component_blom</group>
     <file>env_run.xml</file>
-    <desc>Set the number of sub-cycles for HAMOCC sediment spin-up if HAMOCC_SEDSPINUP == TRUE. 
+    <desc>Set the number of sub-cycles for HAMOCC sediment spin-up if HAMOCC_SEDSPINUP == TRUE.
       Requires module ecosys</desc>
   </entry>
 

diff --git a/cime_config/namelist_definition_blom.xml b/cime_config/namelist_definition_blom.xml
@@ -4135,6 +4135,17 @@
     <desc>add desc</desc>
   </entry>
 
+  <entry id="use_pref_tracers" modify_via_xml="HAMOCC_PREF_TRACERS">
+    <type>logical</type>
+    <category>config_bgc</category>
+    <group>config_bgc</group>
+    <values>
+      <value>.true.</value>
+      <value hamocc_pref_tracers="false">.false.</value>
+    </values>
+    <desc>activate the HAMOCC preformed tracers code</desc>
+  </entry>
+
   <!-- ========================= -->
   <!-- namelist group: bgcoafx -->
   <!-- These options can be activated by expert users via user namelist. -->

diff --git a/hamocc/mo_accfields.F90 b/hamocc/mo_accfields.F90
@@ -128,7 +128,8 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
                                 jsdm_remin_sulf,jsediffnh4,jsediffn2o,jsediffno2,jatmn2o,jatmnh3,  &
                                 jndepnhxfx
     use mo_control_bgc,   only: io_stdo_bgc,dtb,use_BROMO,use_AGG,use_WLIN,use_natDIC,             &
-                                use_CFC,use_sedbypass,use_cisonew,use_BOXATM,use_M4AGO,use_extNcycle
+                                use_CFC,use_sedbypass,use_cisonew,use_BOXATM,use_M4AGO,            &
+                                use_extNcycle,use_pref_tracers
     use mo_param1_bgc,    only: ialkali,ian2o,iano3,iatmco2,iatmdms,iatmn2,iatmn2o,iatmo2,         &
                                 icalc,idet,idms,idicsat,idoc,iiron,iopal,                          &
                                 ioxygen,iphosph,iphy,iprefalk,iprefdic,                            &
@@ -394,12 +395,14 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
     call acclyr(jomegac,OmegaC,pddpo,1)
     call acclyr(jphosy,phosy3d,pddpo,1)
     call acclyr(jo2sat,satoxy,pddpo,1)
-    call acclyr(jprefo2,ocetra(1,1,1,iprefo2),pddpo,1)
-    call acclyr(jprefpo4,ocetra(1,1,1,iprefpo4),pddpo,1)
-    call acclyr(jprefsilica,ocetra(1,1,1,iprefsilica),pddpo,1)
-    call acclyr(jprefalk,ocetra(1,1,1,iprefalk),pddpo,1)
-    call acclyr(jprefdic,ocetra(1,1,1,iprefdic),pddpo,1)
     call acclyr(jdicsat,ocetra(1,1,1,idicsat),pddpo,1)
+    if (use_pref_tracers) then
+      call acclyr(jprefo2,ocetra(1,1,1,iprefo2),pddpo,1)
+      call acclyr(jprefpo4,ocetra(1,1,1,iprefpo4),pddpo,1)
+      call acclyr(jprefsilica,ocetra(1,1,1,iprefsilica),pddpo,1)
+      call acclyr(jprefalk,ocetra(1,1,1,iprefalk),pddpo,1)
+      call acclyr(jprefdic,ocetra(1,1,1,iprefdic),pddpo,1)
+    endif
     if (use_natDIC) then
       call acclyr(jnatalkali,ocetra(1,1,1,inatalkali),pddpo,1)
       call acclyr(jnatdic,ocetra(1,1,1,inatsco212),pddpo,1)
@@ -511,12 +514,14 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
         call acclvl(jlvlomegac,OmegaC,k,ind1,ind2,wghts)
         call acclvl(jlvlphosy,phosy3d,k,ind1,ind2,wghts)
         call acclvl(jlvlo2sat,satoxy,k,ind1,ind2,wghts)
-        call acclvl(jlvlprefo2,ocetra(1,1,1,iprefo2),k,ind1,ind2,wghts)
-        call acclvl(jlvlprefpo4,ocetra(1,1,1,iprefpo4),k,ind1,ind2,wghts)
-        call acclvl(jlvlprefsilica,ocetra(1,1,1,iprefsilica),k,ind1,ind2,wghts)
-        call acclvl(jlvlprefalk,ocetra(1,1,1,iprefalk),k,ind1,ind2,wghts)
-        call acclvl(jlvlprefdic,ocetra(1,1,1,iprefdic),k,ind1,ind2,wghts)
         call acclvl(jlvldicsat,ocetra(1,1,1,idicsat),k,ind1,ind2,wghts)
+        if (use_pref_tracers) then
+          call acclvl(jlvlprefo2,ocetra(1,1,1,iprefo2),k,ind1,ind2,wghts)
+          call acclvl(jlvlprefpo4,ocetra(1,1,1,iprefpo4),k,ind1,ind2,wghts)
+          call acclvl(jlvlprefsilica,ocetra(1,1,1,iprefsilica),k,ind1,ind2,wghts)
+          call acclvl(jlvlprefalk,ocetra(1,1,1,iprefalk),k,ind1,ind2,wghts)
+          call acclvl(jlvlprefdic,ocetra(1,1,1,iprefdic),k,ind1,ind2,wghts)
+        endif
         if (use_natDIC) then
           call acclvl(jlvlnatdic,ocetra(1,1,1,inatsco212),k,ind1,ind2,wghts)
           call acclvl(jlvlnatalkali,ocetra(1,1,1,inatalkali),k,ind1,ind2,wghts)

diff --git a/hamocc/mo_aufr_bgc.F90 b/hamocc/mo_aufr_bgc.F90
@@ -82,7 +82,7 @@ subroutine aufr_bgc(kpie,kpje,kpke,ntr,ntrbgc,itrbgc,trc,kplyear,kplmon,kplday,o
     use mo_carbch,          only: co2star,co3,hi,satoxy,ocetra,atm,nathi
     use mo_control_bgc,     only: io_stdo_bgc,ldtbgc,use_cisonew,use_AGG,                          &
                                   use_BOXATM,use_BROMO,use_CFC,use_natDIC,use_sedbypass,           &
-                                  use_extNcycle
+                                  use_extNcycle,use_pref_tracers
     use mo_param1_bgc,      only: ialkali,ian2o,iano3,icalc,idet,idicsat,                          &
                                   idms,idoc,ifdust,igasnit,iiron,iopal,ioxygen,iphosph,iphy,       &
                                   iprefalk,iprefdic,iprefo2,iprefpo4,iprefsilica,                  &
@@ -400,13 +400,15 @@ subroutine aufr_bgc(kpie,kpje,kpke,ntr,ntrbgc,itrbgc,trc,kplyear,kplmon,kplday,o
     call read_netcdf_var(ncid,'dms',locetra(1,1,1,idms),2*kpke,0,iotype)
     call read_netcdf_var(ncid,'fdust',locetra(1,1,1,ifdust),2*kpke,0,iotype)
     call read_netcdf_var(ncid,'iron',locetra(1,1,1,iiron),2*kpke,0,iotype)
-    call read_netcdf_var(ncid,'prefo2',locetra(1,1,1,iprefo2),2*kpke,0,iotype)
-    call read_netcdf_var(ncid,'prefpo4',locetra(1,1,1,iprefpo4),2*kpke,0,iotype)
-    call read_netcdf_var(ncid,'prefalk',locetra(1,1,1,iprefalk),2*kpke,0,iotype)
-    call read_netcdf_var(ncid,'prefdic',locetra(1,1,1,iprefdic),2*kpke,0,iotype)
     call read_netcdf_var(ncid,'dicsat',locetra(1,1,1,idicsat),2*kpke,0,iotype)
-    if(lread_prefsi) then
-      call read_netcdf_var(ncid,'prefsilica',locetra(1,1,1,iprefsilica),2*kpke,0,iotype)
+    if (use_pref_tracers) then
+      call read_netcdf_var(ncid,'prefo2',locetra(1,1,1,iprefo2),2*kpke,0,iotype)
+      call read_netcdf_var(ncid,'prefpo4',locetra(1,1,1,iprefpo4),2*kpke,0,iotype)
+      call read_netcdf_var(ncid,'prefalk',locetra(1,1,1,iprefalk),2*kpke,0,iotype)
+      call read_netcdf_var(ncid,'prefdic',locetra(1,1,1,iprefdic),2*kpke,0,iotype)
+      if(lread_prefsi) then
+        call read_netcdf_var(ncid,'prefsilica',locetra(1,1,1,iprefsilica),2*kpke,0,iotype)
+      endif
     endif
 
     if (use_cisonew .and. lread_iso) then

diff --git a/hamocc/mo_aufw_bgc.F90 b/hamocc/mo_aufw_bgc.F90
@@ -75,7 +75,8 @@ subroutine aufw_bgc(kpie,kpje,kpke,ntr,ntrbgc,itrbgc,trc,
     use mod_dia,        only: iotype
     use mo_carbch,      only: co2star,co3,hi,satoxy,nathi
     use mo_control_bgc, only: io_stdo_bgc,ldtbgc,rmasks,rmasko,use_cisonew,use_AGG,use_BOXATM,     &
-                              use_BROMO,use_CFC,use_natDIC,use_sedbypass,use_extNcycle
+                              use_BROMO,use_CFC,use_natDIC,use_sedbypass,use_extNcycle,            &
+                              use_pref_tracers
     use mo_sedmnt,      only: sedhpl
     use mo_intfcblom,   only: sedlay2,powtra2,burial2,atm2
     use mo_param1_bgc,  only: ialkali, ian2o,iano3,icalc,idet,idicsat,idms,idoc,ifdust,igasnit,    &
@@ -762,12 +763,14 @@ subroutine aufw_bgc(kpie,kpje,kpke,ntr,ntrbgc,itrbgc,trc,
     call write_netcdf_var(ncid,'dms',locetra(1,1,1,idms),2*kpke,0)
     call write_netcdf_var(ncid,'fdust',locetra(1,1,1,ifdust),2*kpke,0)
     call write_netcdf_var(ncid,'iron',locetra(1,1,1,iiron),2*kpke,0)
-    call write_netcdf_var(ncid,'prefo2',locetra(1,1,1,iprefo2),2*kpke,0)
-    call write_netcdf_var(ncid,'prefpo4',locetra(1,1,1,iprefpo4),2*kpke,0)
-    call write_netcdf_var(ncid,'prefsilica',locetra(1,1,1,iprefsilica),2*kpke,0)
-    call write_netcdf_var(ncid,'prefalk',locetra(1,1,1,iprefalk),2*kpke,0)
-    call write_netcdf_var(ncid,'prefdic',locetra(1,1,1,iprefdic),2*kpke,0)
     call write_netcdf_var(ncid,'dicsat',locetra(1,1,1,idicsat),2*kpke,0)
+    if (use_pref_tracers) then
+      call write_netcdf_var(ncid,'prefo2',locetra(1,1,1,iprefo2),2*kpke,0)
+      call write_netcdf_var(ncid,'prefpo4',locetra(1,1,1,iprefpo4),2*kpke,0)
+      call write_netcdf_var(ncid,'prefsilica',locetra(1,1,1,iprefsilica),2*kpke,0)
+      call write_netcdf_var(ncid,'prefalk',locetra(1,1,1,iprefalk),2*kpke,0)
+      call write_netcdf_var(ncid,'prefdic',locetra(1,1,1,iprefdic),2*kpke,0)
+    endif
     if (use_cisonew) then
       call write_netcdf_var(ncid,'sco213'   ,locetra(1,1,1,isco213) ,2*kpke,0)
       call write_netcdf_var(ncid,'sco214'   ,locetra(1,1,1,isco214) ,2*kpke,0)

diff --git a/hamocc/mo_control_bgc.F90 b/hamocc/mo_control_bgc.F90
@@ -82,6 +82,7 @@ module mo_control_bgc
   logical           :: use_BOXATM             = .false.
   logical           :: use_sedbypass          = .false.
   logical           :: use_extNcycle          = .false.
+  logical           :: use_pref_tracers       = .true.
 
 contains
 

diff --git a/hamocc/mo_hamocc4bcm.F90 b/hamocc/mo_hamocc4bcm.F90
@@ -55,7 +55,7 @@ subroutine hamocc4bcm(kpie,kpje,kpke,kbnd,kplyear,kplmon,kplday,kldtday,pdlxp,pd
                                 do_sedspinup,sedspin_yr_s,sedspin_yr_e,sedspin_ncyc,               &
                                 use_BROMO, use_CFC, use_PBGC_CK_TIMESTEP,                          &
                                 use_BOXATM, use_sedbypass,ocn_co2_type,                            &
-                                do_n2onh3_coupled,use_extNcycle
+                                do_n2onh3_coupled,use_extNcycle,use_pref_tracers
     use mo_param1_bgc,    only: iatmco2,iatmdms,nocetra,nriv,iatmbromo,nndep,iatmn2o,iatmnh3
     use mo_vgrid,         only: set_vgrid
     use mo_apply_fedep,   only: apply_fedep
@@ -309,8 +309,10 @@ subroutine hamocc4bcm(kpie,kpje,kpke,kbnd,kplyear,kplmon,kplday,kldtday,pdlxp,pd
       call inventory_bgc(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask,0)
     endif
 
-    ! update preformed tracers
-    call preftrc(kpie,kpje,omask)
+    if (use_pref_tracers) then
+      ! update preformed tracers
+      call preftrc(kpie,kpje,omask)
+    endif
 
     !--------------------------------------------------------------------
     !     Sediment module

diff --git a/hamocc/mo_ini_fields.F90 b/hamocc/mo_ini_fields.F90
@@ -94,7 +94,7 @@ subroutine ini_fields_ocean(kpaufr,kpie,kpje,kpke,kbnd,pddpo,prho,omask,pglon,pg
     use mo_param_bgc,   only: fesoly,cellmass,fractdim,bifr13_ini,bifr14_ini,c14fac,re1312,re14to
     use mo_biomod,      only: abs_oce
     use mo_control_bgc, only: rmasks,use_FB_BGC_OCE,use_cisonew,use_AGG,use_CFC,use_natDIC,        &
-                              use_BROMO, use_sedbypass,use_extNcycle
+                              use_BROMO, use_sedbypass,use_extNcycle,use_pref_tracers
     use mo_param1_bgc,  only: ialkali,ian2o,iano3,icalc,idet,idicsat,idms,idoc,ifdust,igasnit,     &
                               iiron,iopal,ioxygen,iphosph,iphy,iprefalk,iprefdic,iprefo2,iprefpo4, &
                               isco212,isilica,izoo,iadust,inos,ibromo,icfc11,icfc12,isf6,          &
@@ -190,15 +190,17 @@ subroutine ini_fields_ocean(kpaufr,kpie,kpje,kpke,kbnd,pddpo,prho,omask,pglon,pg
             ocetra(i,j,k,idms)   =0.
             ocetra(i,j,k,ifdust) =0.
             ocetra(i,j,k,iiron)  =fesoly
-            ocetra(i,j,k,iprefo2)=0.
-            ocetra(i,j,k,iprefpo4)=0.
-            ocetra(i,j,k,iprefsilica)=0.
-            ocetra(i,j,k,iprefalk)=0.
-            ocetra(i,j,k,iprefdic)=0.
             ocetra(i,j,k,idicsat)=1.e-8
             hi(i,j,k)            =1.e-8
             co3(i,j,k)           =0.
             co2star(i,j,k)       =20.e-6
+            if (use_pref_tracers) then
+              ocetra(i,j,k,iprefo2)     = 0.
+              ocetra(i,j,k,iprefpo4)    = 0.
+              ocetra(i,j,k,iprefsilica) = 0.
+              ocetra(i,j,k,iprefalk)    = 0.
+              ocetra(i,j,k,iprefdic)    = 0.
+            endif
             if (use_AGG) then
               ! calculate initial numbers from mass, to start with appropriate size distribution
               snow = (ocetra(i,j,k,iphy)+ocetra(i,j,k,idet))*1.e+6
@@ -243,19 +245,21 @@ subroutine ini_fields_ocean(kpaufr,kpie,kpje,kpke,kbnd,pddpo,prho,omask,pglon,pg
       enddo
     enddo
 
-    ! Initialise preformed tracers in the mixed layer; note that the
-    ! whole field has been initialised to zero above
-    do j=1,kpje
-      do i=1,kpie
-        if (omask(i,j) > 0.5) then
-          ocetra(i,j,1:kmle(i,j),iprefo2)  = ocetra(i,j,1:kmle(i,j),ioxygen)
-          ocetra(i,j,1:kmle(i,j),iprefpo4) = ocetra(i,j,1:kmle(i,j),iphosph)
-          ocetra(i,j,1:kmle(i,j),iprefsilica)= ocetra(i,j,1:kmle(i,j),isilica)
-          ocetra(i,j,1:kmle(i,j),iprefalk) = ocetra(i,j,1:kmle(i,j),ialkali)
-          ocetra(i,j,1:kmle(i,j),iprefdic) = ocetra(i,j,1:kmle(i,j),isco212)
-        endif
+    if (use_pref_tracers) then
+      ! Initialise preformed tracers in the mixed layer; note that the
+      ! whole field has been initialised to zero above
+      do j=1,kpje
+        do i=1,kpie
+          if (omask(i,j) > 0.5) then
+            ocetra(i,j,1:kmle(i,j),iprefo2)  = ocetra(i,j,1:kmle(i,j),ioxygen)
+            ocetra(i,j,1:kmle(i,j),iprefpo4) = ocetra(i,j,1:kmle(i,j),iphosph)
+            ocetra(i,j,1:kmle(i,j),iprefsilica)= ocetra(i,j,1:kmle(i,j),isilica)
+            ocetra(i,j,1:kmle(i,j),iprefalk) = ocetra(i,j,1:kmle(i,j),ialkali)
+            ocetra(i,j,1:kmle(i,j),iprefdic) = ocetra(i,j,1:kmle(i,j),isco212)
+          endif
+        enddo
       enddo
-    enddo
+    endif
 
 
     ! Initial values for sediment