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

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Sep 10, 2024
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Making preformed tracers optional to enable HR runs without them #394

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f183a42
Making preformed tracers optional to enable HR runs without them
jmaerz Sep 9, 2024
05121da
string replace preprocessor -> namelist in description
jmaerz Sep 10, 2024
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35 changes: 22 additions & 13 deletions cime_config/config_component.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand All @@ -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">
Expand All @@ -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">
Expand All @@ -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">
Expand All @@ -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>

Expand All @@ -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>

Expand All @@ -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>

Expand Down
11 changes: 11 additions & 0 deletions cime_config/namelist_definition_blom.xml
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Expand Up @@ -4145,6 +4145,17 @@
<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. -->
Expand Down
27 changes: 16 additions & 11 deletions hamocc/mo_accfields.F90
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Expand Up @@ -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, &
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down
16 changes: 9 additions & 7 deletions hamocc/mo_aufr_bgc.F90
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Expand Up @@ -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, &
Expand Down Expand Up @@ -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
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Is there a reason why the preformed silicate is treated differently from the other preformed tracers? Does it make sense to have the capability to restart with a preformed tracer when it is not in the restart file only for silicate but not for the others? I do not see so many use cases for this so maybe we can just omit the lread_prefsi related code?

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@jmaerz jmaerz Sep 10, 2024 •
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Hi Jörg, since preformed silicate wasn't in the restart files before, start-up from restart files was an issue, hence this little quirky treatment that was put in to enable running the model from a restart file without it. Once we settle with #356 or have enough spun-up restart files with preformed silicate, this won't be an issue any longer and it can be removed. Hence, I would keep this treatment for now. We can put this clean-up task into #340 (and #356).

endif

if (use_cisonew .and. lread_iso) then
Expand Down
15 changes: 9 additions & 6 deletions hamocc/mo_aufw_bgc.F90
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Expand Up @@ -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, &
Expand Down Expand Up @@ -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)
Expand Down
1 change: 1 addition & 0 deletions hamocc/mo_control_bgc.F90
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Expand Up @@ -83,6 +83,7 @@ module mo_control_bgc
logical :: use_BOXATM = .false.
logical :: use_sedbypass = .false.
logical :: use_extNcycle = .false.
logical :: use_pref_tracers = .true.

contains

Expand Down
8 changes: 5 additions & 3 deletions hamocc/mo_hamocc4bcm.F90
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
40 changes: 22 additions & 18 deletions hamocc/mo_ini_fields.F90
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Expand Up @@ -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, &
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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