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always obtain ndep from datm or cam using cmeps/cdeps #410

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merged 8 commits into from
Oct 23, 2024
Merged

always obtain ndep from datm or cam using cmeps/cdeps #410

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3a64f47
introduced use_nuopc_ndep to always obtain ndep from mediator
mvertens Sep 29, 2024
c54a2d7
removed some ifdefs from mod_ifdefs and put in mod_xc and updated log…
mvertens Sep 30, 2024
944dd2b
place use_nuopc_ndep in mo_control_bgc
mvertens Oct 2, 2024
457c98f
reverted mod_forcing to master
mvertens Oct 2, 2024
d90b354
fixed namelist issue
mvertens Oct 2, 2024
2b55a4e
fixed computation of ndep update for use_nuopc_ndep is true
mvertens Oct 2, 2024
6032936
more updates addressing comments in PR
mvertens Oct 7, 2024
80c8817
added line break
mvertens Oct 21, 2024
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4 changes: 1 addition & 3 deletions cesm/mod_cesm.F90
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Expand Up @@ -242,7 +242,7 @@ subroutine getfrc_cesm
call ncdefvar('atmbrf_da', 'x y', ndouble, 8)
call ncdefvar('atmn2o_da', 'x y', ndouble, 8)
call ncdefvar('atmnh3_da', 'x y', ndouble, 8)
call ncdefvar('atmnoydep_da', 'x y', ndouble, 8)
call ncdefvar('atmnhxdep_da', 'x y', ndouble, 8)
call ncdefvar('atmnoydep_da', 'x y', ndouble, 8)
call ncdefvar('ztx_da', 'x y', ndouble, 8)
call ncdefvar('mty_da', 'x y', ndouble, 8)
Expand Down Expand Up @@ -301,8 +301,6 @@ subroutine getfrc_cesm
call ncwrtr('mty_da', 'x y', mty_da(1 - nbdy, 1 - nbdy, l2ci), &
iv, 1, 1._r8, 0._r8, 8)
call ncfcls
call xcstop('(getfrc_cesm)')
stop '(getfrc_cesm)'
end if

if (csdiag) then
Expand Down
3 changes: 0 additions & 3 deletions cime_config/buildcpp
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Expand Up @@ -89,9 +89,6 @@ def buildcpp(case):
if pio_typename == "pnetcdf":
blom_cppdefs = blom_cppdefs + " -DPNETCDF"

if ocn_grid in ["tnx2v1", "tnx1.5v1", "tnx1v1", "tnx1v3", "tnx1v4", "tnx0.5v1", "tnx0.25v1", "tnx0.25v3", "tnx0.25v4", "tnx0.125v4"]:
blom_cppdefs = blom_cppdefs + " -DARCTIC"

if ocn_grid in ["gx1v5", "gx1v6", "tnx1v1", "tnx1v3", "tnx1v4", "tnx0.5v1", "tnx0.25v1", "tnx0.25v3", "tnx0.25v4", "tnx0.125v4"]:
blom_cppdefs = blom_cppdefs + " -DLEVITUS2X"

Expand Down
60 changes: 48 additions & 12 deletions cime_config/namelist_definition_blom.xml
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Expand Up @@ -636,17 +636,6 @@
</desc>
</entry>

<entry id="use_stream_relaxation">
<type>logical</type>
<category>limits</category>
<group>limits</group>
<values>
<value>.false.</value>
<value comp_interface="nuopc">.true.</value>
</values>
<desc>if .true., use NUOPC stream relaxation capability</desc>
</entry>

<entry id="trxday">
<type>real</type>
<category>limits</category>
Expand Down Expand Up @@ -903,6 +892,26 @@
<desc>0 = netcdf, 1 = pnetcdf</desc>
</entry>

<entry id="use_diag">
<type>logical</type>
<category>limits</category>
<group>limits</group>
<values>
<value>.false.</value>
</values>
<desc>optionally turn on additional diagnostics</desc>
</entry>

<entry id="use_arctic">
<type>logical</type>
<category>limits</category>
<group>limits</group>
<values>
<value>.true.</value>
</values>
<desc>if region includes arctic ocean</desc>
</entry>

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Question out of curiosity: what is the use_arctic switch for?

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use_arctic has a different communication pattern in mod_xc.F90.
In particular - it checks that all arctic patch tiles must be the same size or empty,
and empty tiles must be "twinned" across the top boundary. It ensures that the latitudinal tile dimension is closed/arctic and handles the halo in the arctic differently. @matsbn - do you want to add more?

<!-- ========================= -->
<!-- namelist group: vcoord -->
<!-- ========================= -->
Expand Down Expand Up @@ -3830,6 +3839,18 @@
<desc>File name (incl. full path) for atmopheric N-deposition data</desc>
</entry>

<entry id="use_nuopc_ndep">
<type>logical</type>
<category>config_bgc</category>
<group>config_bgc</group>
<values>
<value>.false.</value>
<value comp_interface="nuopc">.true.</value>
</values>
<desc>if .true., use NUOPC to obtain NDEP (always imported to model) and ignore the
settings of do_ndep_coupled and ndepfile, whereas the setting of do_ndep is still used</desc>
</entry>

<entry id="do_ndep_coupled" modify_via_xml="HAMOCC_ATMNDEPC">
<type>logical</type>
<category>bgcnml</category>
Expand Down Expand Up @@ -6051,7 +6072,7 @@
<value is_test="yes">0,0,0</value>
<value is_test="yes" empty_hist="yes">0,0,0</value>
</values>
<desc>AMELIST FOR DIAGNOSTIC iHAMOCC OUTPUT</desc>
<desc>namelist for diagnostic iHAMOCC output</desc>
</entry>

<entry id="flx_car0100">
Expand Down Expand Up @@ -8738,6 +8759,21 @@
<desc>(ssster) [mol m-3]</desc>
</entry>

<!-- ========================= -->
<!-- namelist group: forcing fields using nuopc -->
<!-- ========================= -->

<entry id="use_stream_relaxation">
<type>logical</type>
<category>limits</category>
<group>limits</group>
<values>
<value>.false.</value>
<value comp_interface="nuopc">.true.</value>
</values>
<desc>if .true., use NUOPC stream relaxation capability</desc>
</entry>

<!-- ========================= -->
<!-- namelist group: stream_sss -->
<!-- ========================= -->
Expand Down
11 changes: 11 additions & 0 deletions drivers/nuopc/ocn_import_export.F90
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Expand Up @@ -43,6 +43,7 @@ module ocn_import_export
rnf_da, rfi_da, fmltfz_da, sfl_da, ztx_da, mty_da, &
ustarw_da, slp_da, abswnd_da, ficem_da, lamult_da, &
lasl_da, ustokes_da, vstokes_da, atmco2_da, &
atmnhxdep_da, atmnoydep_da, &
l1ci, l2ci
use mod_utility, only: util1, util2
use mod_checksum, only: csdiag, chksummsk
Expand Down Expand Up @@ -142,6 +143,7 @@ module ocn_import_export
index_Faxa_lwdn = -1, &
index_Faxa_snow = -1, &
index_Faxa_rain = -1, &
index_Faxa_ndep = -1, &
index_Sa_pslv = -1, &
index_Sa_co2diag = -1, &
index_Sa_co2prog = -1, &
Expand Down Expand Up @@ -269,6 +271,8 @@ subroutine blom_advertise_imports(flds_scalar_name, fldsToOcn_num, fldsToOcn, &
call fldlist_add(fldsToOcn_num, fldsToOcn, 'Faxa_lwdn' , index_Faxa_lwdn)
call fldlist_add(fldsToOcn_num, fldsToOcn, 'Faxa_snow' , index_Faxa_snow)
call fldlist_add(fldsToOcn_num, fldsToOcn, 'Faxa_rain' , index_Faxa_rain)
call fldlist_add(fldsToOcn_num, fldsToOcn, 'Faxa_ndep' , index_Faxa_ndep, &
ungridded_lbound=1, ungridded_ubound=2)
if (flds_co2a .or. flds_co2c) then
call fldlist_add(fldsToOcn_num, fldsToOcn, 'Sa_co2diag' ,index_Sa_co2diag)
call fldlist_add(fldsToOcn_num, fldsToOcn, 'Sa_co2prog', index_Sa_co2prog)
Expand Down Expand Up @@ -884,6 +888,9 @@ subroutine blom_importflds(fldlist_num, fldlist)
! Ice fraction [].
ficem_da(i,j,l2ci) = fldlist(index_Si_ifrac)%dataptr(n)

! Nitrogen deposition [kg m-2 s-1].
atmnhxdep_da(i,j,l2ci) = fldlist(index_Faxa_ndep)%dataptr2d(1,n)*afac
atmnoydep_da(i,j,l2ci) = fldlist(index_Faxa_ndep)%dataptr2d(2,n)*afac
endif

enddo
Expand All @@ -901,6 +908,8 @@ subroutine blom_importflds(fldlist_num, fldlist)
call xctilr(swa_da(1-nbdy,1-nbdy,l2ci), 1,1, 0,0, halo_ps)
call xctilr(nsf_da(1-nbdy,1-nbdy,l2ci), 1,1, 0,0, halo_ps)
call xctilr(hmlt_da(1-nbdy,1-nbdy,l2ci), 1,1, 0,0, halo_ps)
call xctilr(atmnhxdep_da(1-nbdy,1-nbdy,l2ci), 1,1, 0,0, halo_ps)
call xctilr(atmnoydep_da(1-nbdy,1-nbdy,l2ci), 1,1, 0,0, halo_ps)
endif

call fill_global(mval, fval, halo_ps, slp_da(1-nbdy,1-nbdy,l2ci))
Expand Down Expand Up @@ -1034,6 +1043,8 @@ subroutine blom_importflds(fldlist_num, fldlist)
call chksummsk(abswnd_da(1-nbdy,1-nbdy,l2ci),ip,1,'abswnd')
call chksummsk( ficem_da(1-nbdy,1-nbdy,l2ci),ip,1,'ficem')
call chksummsk(atmco2_da(1-nbdy,1-nbdy,l2ci),ip,1,'atmco2')
call chksummsk(atmnhxdep_da(1-nbdy,1-nbdy,l2ci),ip,1,'atmnhxdep')
call chksummsk(atmnoydep_da(1-nbdy,1-nbdy,l2ci),ip,1,'atmnoydep')
endif

if (first_call) then
Expand Down
1 change: 1 addition & 0 deletions hamocc/mo_control_bgc.F90
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Expand Up @@ -82,6 +82,7 @@ module mo_control_bgc
logical :: use_BOXATM = .false.
logical :: use_sedbypass = .false.
logical :: use_extNcycle = .false.
logical :: use_nuopc_ndep = .false.
logical :: use_pref_tracers = .true.

contains
Expand Down
7 changes: 5 additions & 2 deletions hamocc/mo_hamocc_init.F90
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Expand Up @@ -44,7 +44,8 @@ subroutine hamocc_init(read_rest,rstfnm_hamocc)
dtb,dtbgc,io_stdo_bgc,ldtbgc, &
ldtrunbgc,ndtdaybgc,with_dmsph,l_3Dvarsedpor,use_M4AGO, &
do_ndep_coupled,lkwrbioz_off,do_n2onh3_coupled, &
ocn_co2_type, use_sedbypass, use_BOXATM, use_BROMO,use_extNcycle
ocn_co2_type, use_sedbypass, use_BOXATM, use_BROMO,use_extNcycle, &
use_nuopc_ndep
use mo_param1_bgc, only: ks,init_por2octra_mapping
use mo_param_bgc, only: ini_parambgc
use mo_carbch, only: alloc_mem_carbch,ocetra,atm,atm_co2
Expand Down Expand Up @@ -198,7 +199,9 @@ subroutine hamocc_init(read_rest,rstfnm_hamocc)
! --- Initialise reading of input data (dust, n-deposition, river, etc.)
!
call ini_read_fedep(idm,jdm,omask)
call ini_read_ndep(idm,jdm)
if (.not. use_nuopc_ndep) then
call ini_read_ndep(idm,jdm)
end if
call ini_read_rivin(idm,jdm,omask)
call ini_read_oafx(idm,jdm,bgc_dx,bgc_dy,plat,omask)
if (use_BROMO) then
Expand Down
4 changes: 2 additions & 2 deletions hamocc/mo_param1_bgc.F90
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Expand Up @@ -242,12 +242,12 @@ subroutine init_indices()
use mo_control_bgc, only: bgc_namelist,get_bgc_namelist, io_stdo_bgc
use mo_control_bgc, only: use_BROMO,use_AGG,use_WLIN,use_natDIC,use_CFC,use_cisonew, &
use_sedbypass,use_PBGC_OCNP_TIMESTEP,use_PBGC_CK_TIMESTEP, &
use_FB_BGC_OCE, use_BOXATM,use_extNcycle,use_pref_tracers
use_FB_BGC_OCE, use_BOXATM,use_extNcycle,use_pref_tracers,use_nuopc_ndep
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Could you add a line break here?

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Done.

integer :: iounit

namelist / config_bgc / use_BROMO,use_AGG,use_WLIN,use_natDIC,use_CFC,use_cisonew, &
use_sedbypass,use_PBGC_OCNP_TIMESTEP,use_PBGC_CK_TIMESTEP, &
use_FB_BGC_OCE,use_BOXATM,use_extNcycle,use_pref_tracers
use_FB_BGC_OCE,use_BOXATM,use_extNcycle,use_pref_tracers,use_nuopc_ndep

io_stdo_bgc = lp ! standard out.

Expand Down
57 changes: 35 additions & 22 deletions hamocc/mo_read_ndep.F90
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Expand Up @@ -90,14 +90,14 @@ subroutine ini_read_ndep(kpie,kpje)

! Return if N deposition is turned off
if (.not. do_ndep) then
if (mnproc.eq.1) then
if (mnproc == 1) then
write(io_stdo_bgc,*) ''
write(io_stdo_bgc,*) 'ini_read_ndep: N deposition is not activated.'
endif
return
endif
if (do_ndep_coupled) then
if (mnproc.eq.1) then
if (mnproc == 1) then
write(io_stdo_bgc,*) ''
write(io_stdo_bgc,*) 'ini_read_ndep: N deposition in interactive mode.'
endif
Expand All @@ -107,7 +107,7 @@ subroutine ini_read_ndep(kpie,kpje)
! Initialise the module
if (.not. lini) then

if (mnproc.eq.1) then
if (mnproc == 1) then
write(io_stdo_bgc,*)' '
write(io_stdo_bgc,*)'***************************************************'
write(io_stdo_bgc,*)'iHAMOCC: Initialization of module mo_read_ndep:'
Expand All @@ -116,7 +116,7 @@ subroutine ini_read_ndep(kpie,kpje)

! Check if nitrogen deposition file exists. If not, abort.
inquire(file=ndepfile,exist=file_exists)
if (.not. file_exists .and. mnproc.eq.1) then
if (.not. file_exists .and. mnproc == 1) then
write(io_stdo_bgc,*) ''
write(io_stdo_bgc,*) 'ini_read_ndep: Cannot find N deposition file... '
call xchalt('(ini_read_ndep)')
Expand All @@ -125,32 +125,32 @@ subroutine ini_read_ndep(kpie,kpje)

if (use_extNcycle) then
! Allocate field to hold N-deposition fluxes
if (mnproc.eq.1) then
if (mnproc == 1) then
write(io_stdo_bgc,*)'Memory allocation for variable nhxdepread ...'
write(io_stdo_bgc,*)'First dimension : ',kpie
write(io_stdo_bgc,*)'Second dimension : ',kpje
endif
allocate (nhxdepread(kpie,kpje),stat=errstat)
if(errstat.ne.0) stop 'not enough memory nhxdepread'
if(errstat /= 0) stop 'not enough memory nhxdepread'
nhxdepread(:,:) = 0.0

if (mnproc.eq.1) then
if (mnproc == 1) then
write(io_stdo_bgc,*)'Memory allocation for variable noydepread ...'
write(io_stdo_bgc,*)'First dimension : ',kpie
write(io_stdo_bgc,*)'Second dimension : ',kpje
endif
allocate (noydepread(kpie,kpje),stat=errstat)
if(errstat.ne.0) stop 'not enough memory noydepread'
if(errstat /= 0) stop 'not enough memory noydepread'
noydepread(:,:) = 0.0
else
! Allocate field to hold N-deposition fluxes
if (mnproc.eq.1) then
if (mnproc == 1) then
write(io_stdo_bgc,*)'Memory allocation for variable ndepread ...'
write(io_stdo_bgc,*)'First dimension : ',kpie
write(io_stdo_bgc,*)'Second dimension : ',kpje
endif
allocate (ndepread(kpie,kpje),stat=errstat)
if(errstat.ne.0) stop 'not enough memory ndep'
if(errstat /= 0) stop 'not enough memory ndep'
ndepread(:,:) = 0.0
endif

Expand All @@ -160,7 +160,7 @@ subroutine ini_read_ndep(kpie,kpje)
call ncgeti('endyear',endyear)
call ncfcls

if (mnproc.eq.1) then
if (mnproc == 1) then
write(io_stdo_bgc,*) ''
write(io_stdo_bgc,*) 'ini_read_ndep: Using N deposition file '//trim(ndepfile)
endif
Expand All @@ -182,7 +182,7 @@ subroutine get_ndep(kpie,kpje,kbnd,kplyear,kplmon,omask,ndep,patmnhxdep,patmnoyd

use mod_xc, only: mnproc
use netcdf, only: nf90_open,nf90_close,nf90_nowrite
use mo_control_bgc, only: io_stdo_bgc,do_ndep,use_extNcycle, do_ndep_coupled
use mo_control_bgc, only: io_stdo_bgc, do_ndep, use_extNcycle, do_ndep_coupled, use_nuopc_ndep
use mo_netcdf_bgcrw, only: read_netcdf_var
use mo_param1_bgc, only: nndep,idepnoy,idepnhx
use mo_chemcon, only: mw_nitrogen
Expand All @@ -209,12 +209,14 @@ subroutine get_ndep(kpie,kpje,kbnd,kplyear,kplmon,omask,ndep,patmnhxdep,patmnoyd
return
endif

if (use_extNcycle .and. do_ndep_coupled) then
! If use_nuopc_ndep, nitrogen deposition is ALWAYS obtained from the
! nuopc mediator
if ((use_nuopc_ndep) .or. (use_extNcycle .and. do_ndep_coupled)) then

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Dear @mvertens , I am not fully getting your logics here. If I am not mistaken, the source of N-deposition (whether it comes from CAM or from input files) will be decided at the level of the nuopc, right - so the do_ndep_coupled should appear somewhere else? - currently, the extended nitrogen cycle wouldn't be supported by nupc without the coupled fields to CAM, if I am not mistaken. If so, I would rewrite the code as follows (sorry for the formatting - it's a bit hard on github to keep the overview in a small text box):

if (use_nupc_ndep) then
         ! get N-deposition from atmosphere (either CAM or data)
        ndep(:,:,:) = 0.
        fatmndep = 365.*86400./mw_nitrogen
       
   if (use_extNcycle) then
      !$omp parallel do private(i)
        do j=1,kpje
          do i=1,kpie
            ! convert from kgN/m2/s to climatological input file units: kmolN/m2/yr
            if (patmnoydep(i,j) > 0.) then
              ndep(i,j,idepnoy) = patmnoydep(i,j)*fatmndep
            endif
            if (patmnhxdep(i,j) > 0.) then
              ndep(i,j,idepnhx) = patmnhxdep(i,j)*fatmndep
            endif
          enddo
        enddo
        !$omp end parallel do
        if (mnproc == 1 .and. first_call) then
          write (io_stdo_bgc,*) 'iHAMOCC: getting NOy and NHx deposition from atm'
        endif
   else ! standard N-cycle version
      !$omp parallel do private(i)
        do j=1,kpje
          do i=1,kpie
            ! convert from kgN/m2/s to climatological input file units: kmolN/m2/yr
            ! reduced and oxidized forms will all enter the NO3 pool
            ndep(i,j,idepnoy) = (patmnoydep(i,j)+patmnhxdep(i,j))*fatmndep
          enddo
        enddo
        !$omp end parallel do
   end if
else ! MCT coupler part - don't using nuopc
 ! read ndep data from file
      if (kplmon /= oldmonth) then
        month_in_file=(max(startyear,min(endyear,kplyear))-startyear)*12+kplmon
        if (mnproc == 1) then
          write(io_stdo_bgc,*) 'Read N deposition month ',month_in_file,' from file ',trim(ndepfile)
        endif
        ncstat=nf90_open(trim(ndepfile),nf90_nowrite,ncid)
        if (use_extNcycle) then
          call read_netcdf_var(ncid,'nhxdep',nhxdepread,1,month_in_file,0)
          call read_netcdf_var(ncid,'noydep',noydepread,1,month_in_file,0)
        else
          call read_netcdf_var(ncid,'ndep',ndepread,1,month_in_file,0)
        endif
        ncstat=nf90_close(ncid)
        oldmonth=kplmon
      endif
      !$omp parallel do private(i)
      do j=1,kpje
        do i=1,kpie
             if (use_extNcycle) then
            ndep(i,j,idepnoy) = noydepread(i,j)
            ndep(i,j,idepnhx) = nhxdepread(i,j)
           else
            ndep(i,j,idepnoy) = ndepread(i,j)
          endif
        enddo
      enddo
      !$omp end parallel do

    endif
endif

! get N-deposition from atmosphere
fatmndep = 365.*86400./mw_nitrogen
ndep(:,:,:) = 0.
!$OMP PARALLEL DO PRIVATE(i)
!$omp parallel do private(i)
do j=1,kpje
do i=1,kpie
! convert from kgN/m2/s to climatological input file units: kmolN/m2/yr
Expand All @@ -226,17 +228,28 @@ subroutine get_ndep(kpie,kpje,kbnd,kplyear,kplmon,omask,ndep,patmnhxdep,patmnoyd
endif
enddo
enddo
!$OMP END PARALLEL DO
if (mnproc .eq. 1) then
!$omp end parallel do
if (mnproc == 1) then
write (io_stdo_bgc,*) 'iHAMOCC: getting NOy and NHx deposition from atm'
endif

if (use_nuopc_ndep .and. .not. use_extNcycle) then
! Reduced and oxidized forms will all enter the NO3 pool
!$omp parallel do private(i)
do j=1,kpje
do i=1,kpie
ndep(i,j,idepnoy) = ndep(i,j,idepnoy) + ndep(i,j,idepnhx)
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I am a bit puzzled in this line: if use_extNcycle=.false., ndep is of size (..,..,1) and not (..,..,2) - see mo_param1_bgc. patmnoydep and patmnhxdep hold the fluxes coming from the nuopc cap, right? - hence I would suggest:

ndep(i,j,idepnoy) = (patmnoydep(i,j)+patmnhxdep(i,j))*fatmndep

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I I am not mistaken, this would also affect the former loop above.

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@jmaerz - thanks for catching this. You are totally right. I agree with your suggested change.

enddo
enddo
!$omp end parallel do
end if

else

! read ndep data from file
if (kplmon.ne.oldmonth) then
if (kplmon /= oldmonth) then
month_in_file=(max(startyear,min(endyear,kplyear))-startyear)*12+kplmon
if (mnproc.eq.1) then
if (mnproc == 1) then
write(io_stdo_bgc,*) 'Read N deposition month ',month_in_file,' from file ',trim(ndepfile)
endif
ncstat=nf90_open(trim(ndepfile),nf90_nowrite,ncid)
Expand All @@ -250,10 +263,10 @@ subroutine get_ndep(kpie,kpje,kbnd,kplyear,kplmon,omask,ndep,patmnhxdep,patmnoyd
oldmonth=kplmon
endif

!$OMP PARALLEL DO PRIVATE(i)
!$omp parallel do private(i)
! 1 = NO3; 2 = NH4
do j=1,kpje
do i=1,kpie
do j=1,kpje
do i=1,kpie
if (use_extNcycle) then
ndep(i,j,idepnoy) = noydepread(i,j)
ndep(i,j,idepnhx) = nhxdepread(i,j)
Expand All @@ -262,7 +275,7 @@ subroutine get_ndep(kpie,kpje,kbnd,kplyear,kplmon,omask,ndep,patmnhxdep,patmnoyd
endif
enddo
enddo
!$OMP END PARALLEL DO
!$omp end parallel do

endif
end subroutine get_ndep
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