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Merged
JorgSchwinger merged 1 commit into from
Mar 2, 2026
Merged

Fix some issues with newly added outputs #713

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44 changes: 22 additions & 22 deletions cime_config/namelist_definition_blom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7116,33 +7116,20 @@
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,0,0</value>
<value>0,2,2</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">2,2</value>
</values>
<desc>Surface carbonate ion concentrations [mol C -m3]</desc>
</entry>

<entry id="int_poc">
<entry id="srf_co3satarag">
<type>integer(3)</type>
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,0,0</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">2,2</value>
</values>
<desc>Column-integrated POC concentration [mol P -m2]</desc>
</entry>

<entry id="co3satarag_0">
<type>integer(3)</type>
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,0,0</value>
<value>0,2,2</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">2,2</value>
Expand All @@ -7155,7 +7142,7 @@
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,0,0</value>
<value>0,2,2</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">2,2</value>
Expand All @@ -7168,7 +7155,7 @@
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,0,0</value>
<value>0,2,2</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">2,2</value>
Expand All @@ -7181,7 +7168,7 @@
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,0,0</value>
<value>0,2,2</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">0,0</value>
Expand All @@ -7194,7 +7181,7 @@
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,0,0</value>
<value>0,2,2</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">2,2</value>
Expand All @@ -7207,7 +7194,7 @@
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,0,0</value>
<value>0,2,2</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">2,2</value>
Expand All @@ -7220,14 +7207,27 @@
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,0,0</value>
<value>0,2,2</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">2,2</value>
</values>
<desc>Minimum oxygen concentration in the water column [mol O2 m-3]</desc>
</entry>

<entry id="int_poc">
<type>integer(3)</type>
<category>diabgc</category>
<group>diabgc</group>
<values>
<value>0,2,2</value>
<value is_test="yes">4,2,2</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
<value hamocc_output_size="spinup">2,2</value>
</values>
<desc>Column-integrated POC concentration [mol P -m2]</desc>
</entry>

<entry id="int_bromopro">
<type>integer(3)</type>
<category>diabgc</category>
Expand Down
85 changes: 52 additions & 33 deletions hamocc/mo_accfields.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
jsrfphyto,jsrfsilica,jsrfph,jwnos,jwphy,jndepnoyfx,jtdustfx, &
jsfefx,joalkfx,nbgc,nacc_bgc,bgcwrt,glb_inventory, &
bgct2d,acclvl,acclyr,accsrf,bgczlv, &
jsrfco3,jintpoc,jphyc_200, jco3satarag_0,jph_200,jco3_200, &
jsrfco3,jintpoc,jphyc_200, jsrfco3satarag,jph_200,jco3_200, &
jco3satarag_200,jo2_200,jo2min, &
jatmbromo,jbromo,jbromo_prod,jbromo_uv,jbromofx,jsrfbromo, &
jcfc11,jcfc11fx,jcfc12,jcfc12fx,jsf6,jsf6fx, &
Expand Down Expand Up @@ -153,7 +153,7 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
use_CFC,use_sedbypass,use_cisonew,use_BOXATM,use_M4AGO, &
use_extNcycle,use_pref_tracers,use_shelfsea_res_time, &
use_sediment_quality,use_river2omip,use_DOMclasses
use mo_param1_bgc, only: ialkali,ian2o,iano3,iatmco2,iatmdms,iatmn2,iatmn2o,iatmo2, &
use mo_param1_bgc, only: safediv,ialkali,ian2o,iano3,iatmco2,iatmdms,iatmn2,iatmn2o,iatmo2, &
icalc,idet,idms,idicsat,idoc,iiron,iopal,itdoc_lc,itdoc_hc, &
ioxygen,iphosph,iphy,iprefalk,iprefdic, &
iprefpo4,iprefo2,isco212,isilica,izoo,itdust,isfe, &
Expand All @@ -171,7 +171,7 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
use mo_sedmnt, only: powtra,sedlay,burial,prorca_mavg,sed_reactivity_a, &
sed_reactivity_k,sed_applied_reminrate,sed_rem_aerob,sed_rem_denit,&
sed_rem_sulf
use mo_vgrid, only: dp_min,k0200
use mo_vgrid, only: dp_min,kmle,k0200
use mo_inventory_bgc, only: inventory_bgc
use mo_ncwrt_bgc , only: ncwrt_bgc
use mo_ihamocc4m4ago, only: aggregate_diagnostics,kav_dp,kav_rho_p,kav_d_C,kws_agg,kdf_agg, &
Expand All @@ -192,23 +192,24 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
real(rp), intent(in) :: omask(kpie,kpje) ! land/ocean mask

! Local variables
integer :: i,j,k,l
integer :: i,j,k,k1,l
integer :: ind1(kpie,kpje),ind2(kpie,kpje)
real(rp) :: wghts(kpie,kpje,ddm)
real(rp) :: di12C ! cisonew
real(rp) :: d13C(kpie,kpje,kpke) ! cisonew
real(rp) :: d14C(kpie,kpje,kpke) ! cisonew
real(rp) :: bigd14C(kpie,kpje,kpke) ! cisonew

! CMIP7 additional daily outputs
real(rp) :: di12C
real(rp) :: d13C(kpie,kpje,kpke)
real(rp) :: d14C(kpie,kpje,kpke)
real(rp) :: bigd14C(kpie,kpje,kpke)
real(rp) :: intpoc(kpie,kpje) ! Vertically integrated detritus concentration
real(rp) :: co3satarag_0(kpie,kpje) ! Mole carbonate anion (CO3) for sea water in equilibrium with pure Aragonite @sfc
real(rp) :: srfph(kpie,kpje) ! Temporary variable for calculation of surface pH
real(rp) :: srfco3satarag(kpie,kpje) ! Mole carbonate anion (CO3) for sea water in equilibrium with pure Aragonite @sfc
real(rp) :: phyc_200(kpie,kpje) ! phytoplankton 200m
real(rp) :: ph_200(kpie,kpje) ! pH 200m
real(rp) :: co3_200(kpie,kpje) ! co3 200m
real(rp) :: co3satarag_200(kpie,kpje) ! Mole carbonate anion (CO3) for sea water in equilibrium with pure Aragonite @200m
real(rp) :: o2_200(kpie,kpje) ! o2 200m
real(rp) :: o2min(kpie,kpje) ! in vertical space)
real(rp) :: o2min(kpie,kpje) ! o2 minimum closest to surface

real(rp),parameter :: himin = 1.0e-11 ! Minimum [H+] for calculation of pH

if (use_cisonew) then
! Calculation d13C, d14C and Dd14C: Delta notation for output
Expand All @@ -233,35 +234,51 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
endif

intpoc (:,:)=0._rp
co3satarag_0 (:,:)=0._rp
srfph (:,:)=0._rp
srfco3satarag (:,:)=0._rp
phyc_200 (:,:)=0._rp
ph_200 (:,:)=0._rp
co3_200 (:,:)=0._rp
co3satarag_200(:,:)=0._rp
o2_200 (:,:)=0._rp
o2min (:,:)=0._rp



do j=1,kpje
do i=1,kpie
if(omask(i,j).gt.0.5_rp) then
co3satarag_0(i,j)=co3(i,j,1)/OmegaA(i,j,1)
if(omask(i,j)>0.5_rp) then

srfco3satarag(i,j) = co3(i,j,1)/(OmegaA(i,j,1) + safediv)

k=k0200(i,j)
phyc_200(i,j)=ocetra(i,j,k,iphy)
ph_200(i,j) =-log10(hi(i,j,k))
co3_200(i,j) =co3(i,j,k)
co3satarag_200(i,j)=co3_200(i,j)/OmegaA(i,j,k)
o2_200(i,j) =ocetra(i,j,k,ioxygen)
o2min(i,j) =ocetra(i,j,1,ioxygen)
phyc_200(i,j) = ocetra(i,j,k,iphy)
co3_200(i,j) = co3(i,j,k)
co3satarag_200(i,j) = co3_200(i,j)/(OmegaA(i,j,k) + safediv)
o2_200(i,j) = ocetra(i,j,k,ioxygen)
ph_200(i,j) = -log10(max(hi(i,j,k),himin))

! integrated POC in kmol P m-2
do k=1,kpke
intpoc(i,j) =intpoc(i,j) +ocetra(i,j,k,idet)*pddpo(i,j,k) ! integrated POC in kmol P m-2
o2min(i,j) =min(o2min(i,j),ocetra(i,j,k,ioxygen))
intpoc(i,j) = intpoc(i,j) + ocetra(i,j,k,idet)*pddpo(i,j,k)
enddo
endif

! O2 minimum closest to surface (but below mixed layer)
k1 = kmle(i,j)
o2min(i,j) = ocetra(i,j,k1,ioxygen)
do k=k1+1,kpke
if(pddpo(i,j,k) > dp_min) then
if(o2min(i,j) > ocetra(i,j,k,ioxygen)) then
o2min(i,j) = ocetra(i,j,k,ioxygen)
else
exit
endif
endif
enddo

endif ! omask > 0.5
enddo
enddo


! Accumulated fluxes for inventory.F90. Note that these are currently not written to restart!
! Division by 2 is to account for leap-frog timestepping (but this is not exact)
do j=1,kpje
Expand Down Expand Up @@ -364,7 +381,8 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
call accsrf(jsrfsilica,ocetra(1,1,1,isilica),omask,0)
call accsrf(jsrfdic,ocetra(1,1,1,isco212),omask,0)
call accsrf(jsrfphyto,ocetra(1,1,1,iphy),omask,0)
call accsrf(jsrfph,hi(1,1,1),omask,0)
srfph = -log10(max(hi(:,:,1),himin))
call accsrf(jsrfph,srfph,omask,0)
call accsrf(jdms,ocetra(1,1,1,idms),omask,0)
call accsrf(jsrfpn2om,pn2om,omask,0)
call accsrf(jexport,expoor,omask,0)
Expand All @@ -381,7 +399,7 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
call accsrf(jzeunutlim_n,zeu_nutlim_diag(1,1,inutlim_n),omask,0)
call accsrf(jsrfco3,co3(1,1,1),omask,0)
call accsrf(jintpoc,intpoc,omask,0)
call accsrf(jco3satarag_0,co3satarag_0,omask,0)
call accsrf(jsrfco3satarag,srfco3satarag,omask,0)
call accsrf(jphyc_200,phyc_200,omask,0)
call accsrf(jph_200,ph_200,omask,0)
call accsrf(jco3_200,co3_200,omask,0)
Expand All @@ -392,7 +410,8 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
call accsrf(jsrfnatdic,ocetra(1,1,1,inatsco212),omask,0)
call accsrf(jsrfnatalk,ocetra(1,1,1,inatalkali),omask,0)
call accsrf(jnatpco2,natpco2,omask,0)
call accsrf(jsrfnatph,nathi(1,1,1),omask,0)
srfph = -log10(max(nathi(:,:,1),himin))
call accsrf(jsrfnatph,srfph,omask,0)
endif
if (use_BROMO) then
call accsrf(jsrfbromo,ocetra(1,1,1,ibromo),omask,0)
Expand Down Expand Up @@ -490,7 +509,7 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
call acclyr(jopal,ocetra(1,1,1,iopal),pddpo,1)
call acclyr(jn2o,ocetra(1,1,1,ian2o),pddpo,1)
call acclyr(jco3,co3,pddpo,1)
call acclyr(jph,hi,pddpo,1)
call acclyr(jph,-log10(max(hi,himin)),pddpo,1)
call acclyr(jomegaa,OmegaA,pddpo,1)
call acclyr(jomegac,OmegaC,pddpo,1)
call acclyr(jphosy,phosy3d,pddpo,1)
Expand All @@ -511,7 +530,7 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
call acclyr(jnatdic,ocetra(1,1,1,inatsco212),pddpo,1)
call acclyr(jnatcalc,ocetra(1,1,1,inatcalc),pddpo,1)
call acclyr(jnatco3,natco3,pddpo,1)
call acclyr(jnatph,nathi,pddpo,1)
call acclyr(jnatph,-log10(max(nathi,himin)),pddpo,1)
call acclyr(jnatomegaa,natOmegaA,pddpo,1)
call acclyr(jnatomegac,natOmegaC,pddpo,1)
endif
Expand Down Expand Up @@ -639,7 +658,7 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
call acclvl(jlvlopal,ocetra(1,1,1,iopal),k,ind1,ind2,wghts)
call acclvl(jlvln2o,ocetra(1,1,1,ian2o),k,ind1,ind2,wghts)
call acclvl(jlvlco3,co3,k,ind1,ind2,wghts)
call acclvl(jlvlph,hi,k,ind1,ind2,wghts)
call acclvl(jlvlph,-log10(max(hi,himin)),k,ind1,ind2,wghts)
call acclvl(jlvlomegaa,OmegaA,k,ind1,ind2,wghts)
call acclvl(jlvlomegac,OmegaC,k,ind1,ind2,wghts)
call acclvl(jlvlphosy,phosy3d,k,ind1,ind2,wghts)
Expand All @@ -660,7 +679,7 @@ subroutine accfields(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
call acclvl(jlvlnatalkali,ocetra(1,1,1,inatalkali),k,ind1,ind2,wghts)
call acclvl(jlvlnatcalc,ocetra(1,1,1,inatcalc),k,ind1,ind2,wghts)
call acclvl(jlvlnatco3,natco3,k,ind1,ind2,wghts)
call acclvl(jlvlnatph,nathi,k,ind1,ind2,wghts)
call acclvl(jlvlnatph,-log10(max(nathi,himin)),k,ind1,ind2,wghts)
call acclvl(jlvlnatomegaa,natOmegaA,k,ind1,ind2,wghts)
call acclvl(jlvlnatomegac,natOmegaC,k,ind1,ind2,wghts)
endif
Expand Down
24 changes: 12 additions & 12 deletions hamocc/mo_bgcmean.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -116,10 +116,10 @@ module mo_bgcmean
& SRF_ATMBROMO =0 ,SRF_BROMO =0 ,SRF_BROMOFX =0 , &
& SRF_ANH4 =0 ,SRF_ANO2 =0 ,SRF_ANH3FX =0 , &
& SRF_PN2OM =0 ,SRF_PNH3 =0 ,SRF_ATMNH3 =0 , &
& SRF_ATMN2O =0 ,SRF_CO3 =0 ,INT_BROMOPRO =0 , &
& INT_BROMOUV =0 ,INT_POC =0 ,CO3SATARAG_0 =0 , &
& SRF_ATMN2O =0 ,SRF_CO3 =0 ,SRF_CO3SATARAG=0 , &
& PHYC_200 =0 ,PH_200 =0 ,CO3_200 =0 , &
& CO3SATARAG_200=0 ,O2_200 =0 ,O2MIN =0 , &
& INT_BROMOPRO =0 ,INT_BROMOUV =0 ,INT_POC =0 , &
& INT_PHOSY =0 ,INT_NFIX =0 ,INT_DNIT =0 , &
& INT_EXUDL =0 ,INT_EXUDSL =0 ,INT_EXCRL =0 , &
& INT_EXCRSL =0 ,INT_DOCL_REM =0 ,INT_DOCSL_REM =0 , &
Expand Down Expand Up @@ -254,10 +254,10 @@ module mo_bgcmean
& SRF_ATMBROMO ,SRF_BROMO ,SRF_BROMOFX , &
& SRF_ANH4 ,SRF_ANO2 ,SRF_ANH3FX , &
& SRF_PN2OM ,SRF_PNH3 ,SRF_ATMNH3 , &
& SRF_ATMN2O ,SRF_CO3 ,INT_BROMOPRO , &
& INT_BROMOUV ,INT_POC ,CO3SATARAG_0 , &
& SRF_ATMN2O ,SRF_CO3 ,SRF_CO3SATARAG , &
& PHYC_200 ,PH_200 ,CO3_200 , &
& CO3SATARAG_200 ,O2_200 ,O2MIN , &
& INT_BROMOPRO ,INT_BROMOUV ,INT_POC , &
& INT_PHOSY ,INT_NFIX ,INT_DNIT , &
& INT_EXUDL ,INT_EXUDSL ,INT_EXCRL , &
& INT_EXCRSL ,INT_DOCL_REM ,INT_DOCSL_REM , &
Expand Down Expand Up @@ -436,6 +436,8 @@ module mo_bgcmean
& jsrfdic = 0 , &
& jsrfphyto = 0 , &
& jsrfph = 0 , &
& jsrfco3 = 0 , &
& jsrfco3satarag= 0 , &
& jintphosy = 0 , &
& jintnfix = 0 , &
& jintdnit = 0 , &
Expand Down Expand Up @@ -480,8 +482,6 @@ module mo_bgcmean
& jzeunutlim_fe = 0 , &
& jzeunutlim_phosph = 0 , &
& jzeunutlim_n = 0 , &
& jsrfco3 = 0 , &
& jco3satarag_0 = 0 , &
& jphyc_200 = 0 , &
& jph_200 = 0 , &
& jco3_200 = 0 , &
Expand Down Expand Up @@ -932,6 +932,12 @@ subroutine alloc_mem_bgcmean(kpie,kpje,kpke)
jsrfphyto(n)=i_bsc_m2d*min(1,SRF_PHYTO(n))
if (SRF_PH(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jsrfph(n)=i_bsc_m2d*min(1,SRF_PH(n))
if (SRF_CO3(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jsrfco3(n)=i_bsc_m2d*min(1,SRF_CO3(n))
if (SRF_CO3SATARAG(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jsrfco3satarag(n)=i_bsc_m2d*min(1,SRF_CO3SATARAG(n))
if (INT_POC(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jintpoc(n)=i_bsc_m2d*min(1,INT_POC(n))
if (INT_PHOSY(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jintphosy(n)=i_bsc_m2d*min(1,INT_PHOSY(n))
if (INT_NFIX(n) > 0) i_bsc_m2d=i_bsc_m2d+1
Expand Down Expand Up @@ -1000,12 +1006,6 @@ subroutine alloc_mem_bgcmean(kpie,kpje,kpke)
jzeunutlim_phosph(n)=i_bsc_m2d*min(1,ZEU_NUTLIM_PHOSPH(n))
if (ZEU_NUTLIM_N(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jzeunutlim_N(n)=i_bsc_m2d*min(1,ZEU_NUTLIM_N(n))
if (SRF_CO3(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jsrfco3(n)=i_bsc_m2d*min(1,SRF_CO3(n))
if (INT_POC(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jintpoc(n)=i_bsc_m2d*min(1,INT_POC(n))
if (CO3SATARAG_0(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jco3satarag_0(n)=i_bsc_m2d*min(1,CO3SATARAG_0(n))
if (PHYC_200(n) > 0) i_bsc_m2d=i_bsc_m2d+1
jphyc_200(n)=i_bsc_m2d*min(1,PHYC_200(n))
if (PH_200(n) > 0) i_bsc_m2d=i_bsc_m2d+1
Expand Down
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