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Feature hamocc sediment spinup #162

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May 18, 2022
Merged

Feature hamocc sediment spinup #162

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f3fe468
Add sediment spin-up option
JorgSchwinger May 11, 2022
e160331
Merge branch 'master' into feature-hamocc_sediment_spinup
JorgSchwinger May 11, 2022
b160abd
remaining changes and bug fixes for sediment acceleration
JorgSchwinger May 12, 2022
3d9e2cd
Re-set silicate dissolution rate in the sediment for CMIP6 backwards …
JorgSchwinger May 12, 2022
241328a
Merge branch 'master' into feature-hamocc_sediment_spinup
JorgSchwinger May 12, 2022
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99 changes: 72 additions & 27 deletions cime_config/buildnml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,10 @@ set BLOM_N_DEPOSITION = `./xmlquery BLOM_N_DEPOSITION --value`
set BLOM_NDEP_SCENARIO = `./xmlquery BLOM_NDEP_SCENARIO --value`
set HAMOCC_VSLS = `./xmlquery HAMOCC_VSLS --value`
set HAMOCC_CISO = `./xmlquery HAMOCC_CISO --value`
set HAMOCC_SEDSPINUP = `./xmlquery HAMOCC_SEDSPINUP --value`
set HAMOCC_SEDSPINUP_YR_START = `./xmlquery HAMOCC_SEDSPINUP_YR_START --value`
set HAMOCC_SEDSPINUP_YR_END = `./xmlquery HAMOCC_SEDSPINUP_YR_END --value`
set HAMOCC_SEDSPINUP_NCYCLE = `./xmlquery HAMOCC_SEDSPINUP_NCYCLE --value`
set RUN_STARTDATE = `./xmlquery RUN_STARTDATE --value`
set PIO_TYPENAME_OCN = `./xmlquery PIO_TYPENAME_OCN --value`
set PIO_NETCDF_FORMAT_OCN = `./xmlquery PIO_NETCDF_FORMAT_OCN --value`
Expand Down Expand Up @@ -185,6 +189,17 @@ else
set DO_NDEP = .false.
set NDEPFNAME = ""
endif
if ($HAMOCC_SEDSPINUP == TRUE) then
set DO_SEDSPINUP = .true.
set SEDSPIN_YR_S = $HAMOCC_SEDSPINUP_YR_START
set SEDSPIN_YR_E = $HAMOCC_SEDSPINUP_YR_END
set SEDSPIN_NCYC = $HAMOCC_SEDSPINUP_NCYCLE
else
set DO_SETSPINUP = .false.
set SEDSPIN_YR_S = -1
set SEDSPIN_YR_E = -1
set SEDSPIN_NCYC = -1
endif
# VSLS is currently only available for the tnx1v4 grid, since a climatlogy file for
# short wave radiation is needed.
if ($HAMOCC_VSLS == TRUE && $OCN_GRID != tnx1v4) then
Expand Down Expand Up @@ -524,6 +539,13 @@ set LVL_WNOS = '0, 2, 2'
set LVL_EPS = '0, 0, 0'
set LVL_ASIZE = '0, 0, 0'
set LVL_BROMO = '0, 2, 2'
set FLX_SEDIFFIC = '0, 0, 2'
set FLX_SEDIFFAL = '0, 0, 2'
set FLX_SEDIFFPH = '0, 0, 2'
set FLX_SEDIFFOX = '0, 0, 2'
set FLX_SEDIFFN2 = '0, 0, 2'
set FLX_SEDIFFNO3 = '0, 0, 2'
set FLX_SEDIFFSI = '0, 0, 2'
set SDM_POWAIC = '0, 0, 2'
set SDM_POWAAL = '0, 0, 2'
set SDM_POWAPH = '0, 0, 2'
Expand Down Expand Up @@ -1336,32 +1358,40 @@ cat >>! $RUNDIR/ocn_in$inststr << EOF
!
! CONTENTS:
!
! ATM_CO2 : Atmospheric CO2 concentration [ppmv]
! FEDEPFILE : File name (incl. full path) for iron (dust) deposition data
! SWACLIMFILE : File name (incl. full path) for swa climatology field (needed
! if bromoform scheme is activated)
! DO_RIVINPT : Logical switch to activate riverine input
! RIVINFILE : File name (incl. full path) for riverine input data
! DO_NDEP : Logical switch to activate N-deposition
! NDEPFILE : File name (incl. full path) for atmopheric N-deposition data
! INIXXX : Initial condition file for iHAMOCC, where XXX=DIC, ALK, PO4,
! OXY, NO3, SIL, D13C, and D14C
! ATM_CO2 : Atmospheric CO2 concentration [ppmv]
! FEDEPFILE : File name (incl. full path) for iron (dust) deposition data
! SWACLIMFILE : File name (incl. full path) for swa climatology field (needed
! if bromoform scheme is activated)
! DO_RIVINPT : Logical switch to activate riverine input
! RIVINFILE : File name (incl. full path) for riverine input data
! DO_NDEP : Logical switch to activate N-deposition
! NDEPFILE : File name (incl. full path) for atmopheric N-deposition data
! DO_SEDSPINUP : Logical switch to activate sediment spin-up
! SEDSPIN_YR_S : Start year for sediment spinup
! SEDSPIN_YR_E : End year for sediment spinup
! SEDSPIN_NCYC : Number of subcyles per time-step for sediment spinup
! INIXXX : Initial condition file for iHAMOCC, where XXX=DIC, ALK, PO4,
! OXY, NO3, SIL, D13C, and D14C
&BGCNML
ATM_CO2 = $CCSM_CO2_PPMV
FEDEPFILE = $FEDEPFILE
SWACLIMFILE= $SWACLIMFILE
DO_RIVINPT = $DO_RIVINPT
RIVINFILE = $RIVINFILE
DO_NDEP = $DO_NDEP
NDEPFILE = $NDEPFILE
INIDIC = $INIDIC
INIALK = $INIALK
INIPO4 = $INIPO4
INIOXY = $INIOXY
ININO3 = $ININO3
INISIL = $INISIL
INID13C = $INID13C
INID14C = $INID14C
ATM_CO2 = $CCSM_CO2_PPMV
FEDEPFILE = $FEDEPFILE
SWACLIMFILE = $SWACLIMFILE
DO_RIVINPT = $DO_RIVINPT
RIVINFILE = $RIVINFILE
DO_NDEP = $DO_NDEP
NDEPFILE = $NDEPFILE
DO_SEDSPINUP = $DO_SEDSPINUP
SEDSPIN_YR_S = $SEDSPIN_YR_S
SEDSPIN_YR_E = $SEDSPIN_YR_E
SEDSPIN_NCYC = $SEDSPIN_NCYC
INIDIC = $INIDIC
INIALK = $INIALK
INIPO4 = $INIPO4
INIOXY = $INIOXY
ININO3 = $ININO3
INISIL = $INISIL
INID13C = $INID13C
INID14C = $INID14C
/

! IO-NAMELIST FOR DIAGNOSTIC iHAMOCC OUTPUT
Expand Down Expand Up @@ -1485,11 +1515,19 @@ cat >>! $RUNDIR/ocn_in$inststr << EOF
! NFIX - Vertically integrated nitrogen fixation
! DNIT - Vertically integrated denitrification
!
! Particle fluxes (FLX, where ****=0100,0500,1000,2000,4000, or _BOT)
! Particle fluxes (FLX, e.g CARFLX****, where ****=0100,0500,1000,2000,4000, or _BOT)
! and diffusive fluxes at the sediment - water-column interface (SEDIFF*)
! CARFLX**** - POC flux at **** metres depth [mol C m-2 s-1]
! BSIFLX**** - Biogenic silica flux at **** metres depth [mol Si m-2 s-1]
! CALFLX**** - Calcium carbonate flux at **** metres depth [mol C m-2 s-1]
!
! SEDIFFIC - sediment - water-column diffusive flux of DIC [mol C m-2 s-1]
! SEDIFFAL - sediment - water-column diffusive flux of alkalinity [mol m-2 s-1]
! SEDIFFPH - sediment - water-column diffusive flux of phosphate [mol PO3 m-2 s-1]
! SEDIFFOX - sediment - water-column diffusive flux of oxygen [mol O2 m-2 s-1]
! SEDIFFN2 - sediment - water-column diffusive flux of N2 [mol N2 m-2 s-1]
! SEDIFFNO3 - sediment - water-column diffusive flux of nitrate [mol NO3 m-2 s-1]
! SEDIFFSI - sediment - water-column diffusive flux of silica [mol Si m-2 s-1]
!
! Sediment fields (SDM)
! POWAIC - (powdic) [mol C m-3]
! POWAAL - (powalk) [eq m-3]
Expand Down Expand Up @@ -1679,6 +1717,13 @@ cat >>! $RUNDIR/ocn_in$inststr << EOF
LVL_EPS = $LVL_EPS
LVL_ASIZE = $LVL_ASIZE
LVL_BROMO = $LVL_BROMO
FLX_SEDIFFIC = $FLX_SEDIFFIC
FLX_SEDIFFAL = $FLX_SEDIFFAL
FLX_SEDIFFPH = $FLX_SEDIFFPH
FLX_SEDIFFOX = $FLX_SEDIFFOX
FLX_SEDIFFN2 = $FLX_SEDIFFN2
FLX_SEDIFFNO3 = $FLX_SEDIFFNO3
FLX_SEDIFFSI = $FLX_SEDIFFSI
SDM_POWAIC = $SDM_POWAIC
SDM_POWAAL = $SDM_POWAAL
SDM_POWAPH = $SDM_POWAPH
Expand Down
40 changes: 40 additions & 0 deletions cime_config/config_component.xml
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Expand Up @@ -147,7 +147,47 @@
<file>env_build.xml</file>
<desc>Set preprocessor option to activate the carbon isotope code. Requires module ecosys</desc>
</entry>

<entry id="HAMOCC_SEDSPINUP">
<type>logical</type>
<valid_values>TRUE,FALSE</valid_values>
<default_value>FALSE</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
need to be set to valid values for this option to take effect. Requires module ecosys</desc>
</entry>

<entry id="HAMOCC_SEDSPINUP_YR_START">
<type>integer</type>
<valid_values/>
<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.
Requires module ecosys</desc>
</entry>

<entry id="HAMOCC_SEDSPINUP_YR_END">
<type>integer</type>
<valid_values/>
<default_value>-1</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.
Requires module ecosys</desc>
</entry>

<entry id="HAMOCC_SEDSPINUP_NCYCLE">
<type>integer</type>
<valid_values/>
<default_value>-1</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.
Requires module ecosys</desc>
</entry>

<entry id="HAMOCC_VSLS">
<type>logical</type>
<valid_values>TRUE,FALSE</valid_values>
Expand Down
23 changes: 23 additions & 0 deletions hamocc/accfields.F90
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Expand Up @@ -99,10 +99,23 @@ SUBROUTINE ACCFIELDS(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
do i=1,kpie
if(omask(i,j).gt.0.5) then

! Atmosphere-ocean fluxes
bgct2d(i,j,jco2flux) = bgct2d(i,j,jco2flux) + atmflx(i,j,iatmco2)/2.0
bgct2d(i,j,jo2flux) = bgct2d(i,j,jo2flux) + atmflx(i,j,iatmo2)/2.0
bgct2d(i,j,jn2flux) = bgct2d(i,j,jn2flux) + atmflx(i,j,iatmn2)/2.0
bgct2d(i,j,jn2oflux) = bgct2d(i,j,jn2oflux) + atmflx(i,j,iatmn2o)/2.0
! Particle fluxes between water-column and sediment
bgct2d(i,j,jprorca) = bgct2d(i,j,jprorca) + carflx_bot(i,j)/2.0
bgct2d(i,j,jprcaca) = bgct2d(i,j,jprcaca) + calflx_bot(i,j)/2.0
bgct2d(i,j,jsilpro) = bgct2d(i,j,jsilpro) + bsiflx_bot(i,j)/2.0
! Diffusive fluxes between water-column and sediment
bgct2d(i,j,jpodiic) = bgct2d(i,j,jpodiic) + sedfluxo(i,j,ipowaic)/2.0
bgct2d(i,j,jpodial) = bgct2d(i,j,jpodial) + sedfluxo(i,j,ipowaal)/2.0
bgct2d(i,j,jpodiph) = bgct2d(i,j,jpodiph) + sedfluxo(i,j,ipowaph)/2.0
bgct2d(i,j,jpodiox) = bgct2d(i,j,jpodiox) + sedfluxo(i,j,ipowaox)/2.0
bgct2d(i,j,jpodin2) = bgct2d(i,j,jpodin2) + sedfluxo(i,j,ipown2)/2.0
bgct2d(i,j,jpodino3) = bgct2d(i,j,jpodino3) + sedfluxo(i,j,ipowno3)/2.0
bgct2d(i,j,jpodisi) = bgct2d(i,j,jpodisi) + sedfluxo(i,j,ipowasi)/2.0

endif
enddo
Expand Down Expand Up @@ -200,6 +213,16 @@ SUBROUTINE ACCFIELDS(kpie,kpje,kpke,pdlxp,pdlyp,pddpo,omask)
call accsrf(jcalflx_bot,calflx_bot,omask,0)
ENDIF

! Accumulate diffusive fluxes between water column and sediment
call accsrf(jsediffic,sedfluxo(1,1,ipowaic),omask,0)
call accsrf(jsediffal,sedfluxo(1,1,ipowaal),omask,0)
call accsrf(jsediffph,sedfluxo(1,1,ipowaph),omask,0)
call accsrf(jsediffox,sedfluxo(1,1,ipowaox),omask,0)
call accsrf(jsediffn2,sedfluxo(1,1,ipown2),omask,0)
call accsrf(jsediffno3,sedfluxo(1,1,ipowno3),omask,0)
call accsrf(jsediffsi,sedfluxo(1,1,ipowasi),omask,0)


! Accumulate layer diagnostics
call acclyr(jdp,pddpo,pddpo,0)
call acclyr(jphyto,ocetra(1,1,1,iphy),pddpo,1)
Expand Down
15 changes: 8 additions & 7 deletions hamocc/dipowa.F90
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Expand Up @@ -17,7 +17,7 @@
! along with BLOM. If not, see https://www.gnu.org/licenses/.


subroutine dipowa(kpie,kpje,kpke,omask)
subroutine dipowa(kpie,kpje,kpke,omask,lspin)
!**********************************************************************
!
!**** *DIPOWA* - 'diffusion of pore water'
Expand Down Expand Up @@ -65,7 +65,8 @@ subroutine dipowa(kpie,kpje,kpke,omask)
implicit none

integer, intent(in) :: kpie, kpje, kpke
real, dimension(kpie,kpje), intent(in) :: omask
real, intent(in) :: omask(kpie,kpje)
logical, intent(in) :: lspin

! Local variables
integer :: i,j,k,l,iv
Expand Down Expand Up @@ -170,7 +171,6 @@ subroutine dipowa(kpie,kpje,kpke,omask)
enddo
enddo

! call maschk(kpie,kpje,kpke,23)
! sediment column
do iv = 1,npowtra
do k = 1,ks-1
Expand All @@ -183,8 +183,8 @@ subroutine dipowa(kpie,kpje,kpke,omask)
enddo
enddo
enddo
! call maschk(kpie,kpje,kpke,24)

if(.not. lspin) THEN
! sediment ocean interface
!
! CAUTION - the following assumes same indecees for ocetra and powtra
Expand All @@ -204,9 +204,9 @@ subroutine dipowa(kpie,kpje,kpke,omask)
& ( sedb1(i,l,iv) - tredsy(i,l,3) * powtra(i,j,l+1,iv) ) &
& / tredsy(i,l,2)

! used in inventory_bgc/maschk (diagnostics)
! diffusive fluxes (positive downward)
sedfluxo(i,j,iv) = sedfluxo(i,j,iv) &
& + ocetra(i,j,kbo(i,j),iv) - aprior
& -(ocetra(i,j,kbo(i,j),iv) - aprior)* bolay(i,j)
Comment on lines 212 to +213
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Should this be without accumulation in sedfluxo?

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I think this is correct as it is: In powach sedfluxo is set to zero when entering the sediment. Then it is receiving a value for silicate and oxygen (but not the others) in powach. After that dipowa is called, where sedfluxo is updated in a loop. In order to avoid overwriting the values for oxygen and silicate, it is written as above.

#ifdef natDIC
if (iv==isco212) ocetra(i,j,kbo(i,j),inatsco212) = &
& ocetra(i,j,kbo(i,j),inatsco212) + &
Expand All @@ -218,8 +218,9 @@ subroutine dipowa(kpie,kpje,kpke,omask)
endif
enddo
enddo
! call maschk(kpie,kpje,kpke,25)

endif ! .not. lspin

enddo j_loop

end subroutine dipowa
30 changes: 27 additions & 3 deletions hamocc/hamocc4bcm.F90
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Expand Up @@ -122,6 +122,8 @@ SUBROUTINE HAMOCC4BCM(kpie,kpje,kpke,kbnd,kplyear,kplmon,kplday,kldtday,&
REAL, intent(out) :: pflxbromo(1-kbnd:kpie+kbnd,1-kbnd:kpje+kbnd)

INTEGER :: i,j,k,l
INTEGER :: nspin,it
LOGICAL :: lspin

IF (mnproc.eq.1) THEN
write(io_stdo_bgc,*) 'iHAMOCC',KLDTDAY,LDTRUNBGC,NDTDAYBGC
Expand Down Expand Up @@ -173,7 +175,7 @@ SUBROUTINE HAMOCC4BCM(kpie,kpje,kpke,kbnd,kplyear,kplmon,kplday,kldtday,&
#endif

#ifdef BROMO
!$OMP PARALLEL DO
!$OMP PARALLEL DO PRIVATE(i)
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Separate openMP bugfix?

DO j=1,kpje
DO i=1,kpie
IF (patmbromo(i,j).gt.0.) THEN
Expand Down Expand Up @@ -293,8 +295,30 @@ SUBROUTINE HAMOCC4BCM(kpie,kpje,kpke,kbnd,kplyear,kplmon,kplday,kldtday,&
#ifndef sedbypass
! jump over sediment if sedbypass is defined

CALL POWACH(kpie,kpje,kpke,kbnd,prho,omask,psao)
if(do_sedspinup .and. kplyear>=sedspin_yr_s &
.and. kplyear<=sedspin_yr_e) then
nspin = sedspin_ncyc
if(mnproc == 1) then
write(io_stdo_bgc,*)
write(io_stdo_bgc,*) 'iHAMOCC: sediment spinup activated with ', &
nspin, ' subcycles'
endif
else
nspin = 1
endif

! Loop for sediment spinup. If deactivated then nspin=1 and lspin=.false.
do it=1,nspin

if( it<nspin ) then
lspin=.true.
else
lspin=.false.
endif

call POWACH(kpie,kpje,kpke,kbnd,prho,omask,psao,lspin)

enddo

#ifdef PBGC_CK_TIMESTEP
IF (mnproc.eq.1) THEN
Expand Down Expand Up @@ -353,7 +377,7 @@ SUBROUTINE HAMOCC4BCM(kpie,kpje,kpke,kbnd,kplyear,kplmon,kplday,kldtday,&
!--------------------------------------------------------------------
! Pass bromoform flux. Convert unit from kmol CHBr3/m^2 to kg/m^2/s.
! Negative values to the atmosphere
!$OMP PARALLEL DO
!$OMP PARALLEL DO PRIVATE(i)
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Separate openMP bugfix?

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I agree, I should have done this in a separate commit, but now I don't have the time to disentangle this so I'll leave it as it is.

DO j=1,kpje
DO i=1,kpie
if(omask(i,j) .gt. 0.5) pflxbromo(i,j)=-252.7*atmflx(i,j,iatmbromo)/dtbgc
Expand Down
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