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Merge pull request #410 from mvertens/feature/ndep_from_cmeps
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always obtain ndep from datm or cam using cmeps/cdeps
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@jmaerz
jmaerz authored Oct 23, 2024
2 parents cbca1a6 + 80c8817 commit 6710b58
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Showing 14 changed files with 176 additions and 148 deletions.
4 changes: 1 addition & 3 deletions cesm/mod_cesm.F90
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Original file line number Diff line number Diff line change
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
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3 changes: 0 additions & 3 deletions cime_config/buildcpp
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Original file line number Diff line number Diff line change
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"

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32 changes: 17 additions & 15 deletions cime_config/config_component.xml
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Expand Up @@ -121,23 +121,24 @@
<valid_values>UNSET,1850,2000,hist,ssp119,ssp126,ssp245,ssp370,ssp434,ssp460,ssp534os,ssp585</valid_values>
<default_value>1850</default_value>
<values>
<value compset="HIST_CAM60%NORESM.*_BLOM%ECO" >hist</value>
<value compset="20TR_DATM.*_BLOM%ECO" >hist</value>
<value compset="2000_CAM60%NORESM.*_BLOM%ECO" >2000</value>
<value compset="SSP119_CAM60%NORESM.*_BLOM%ECO" >ssp119</value>
<value compset="SSP126_CAM60%NORESM.*_BLOM%ECO" >ssp126</value>
<value compset="SSP245_CAM60%NORESM.*_BLOM%ECO" >ssp245</value>
<value compset="SSP370_CAM60%NORESM.*_BLOM%ECO" >ssp370</value>
<value compset="SSP370LOWNTCF_CAM60%NORESM.*_BLOM%ECO" >ssp370</value>
<value compset="SSP370REFGHGLOWNTCF_CAM60%NORESM.*_BLOM%ECO">ssp370</value>
<value compset="SSP434_CAM60%NORESM.*_BLOM%ECO" >ssp434</value>
<value compset="SSP460_CAM60%NORESM.*_BLOM%ECO" >ssp460</value>
<value compset="SSP534_CAM60%NORESM.*_BLOM%ECO" >ssp534os</value>
<value compset="SSP585_CAM60%NORESM.*_BLOM%ECO" >ssp585</value>
<value compset="1850_.*_BLOM%ECO" >1850</value>
<value compset="2000_.*_BLOM%ECO" >2000</value>
<value compset="HIST_.*_BLOM%ECO" >hist</value>
<value compset="20TR_.*_BLOM%ECO" >hist</value>
<value compset="SSP119_.*_BLOM%ECO" >ssp119</value>
<value compset="SSP126_.*_BLOM%ECO" >ssp126</value>
<value compset="SSP245_.*_BLOM%ECO" >ssp245</value>
<value compset="SSP370_.*_BLOM%ECO" >ssp370</value>
<value compset="SSP434_.*_BLOM%ECO" >ssp434</value>
<value compset="SSP460_.*_BLOM%ECO" >ssp460</value>
<value compset="SSP534_.*_BLOM%ECO" >ssp534os</value>
<value compset="SSP585_.*_BLOM%ECO" >ssp585</value>
<value compset="SSP370.*_BLOM%ECO" >ssp370</value>
</values>
<group>run_component_blom</group>
<file>env_run.xml</file>
<desc>Scenario for nitrogen deposition data. Requires module ecosys</desc>
<desc>Scenario for nitrogen deposition data. Requires module ecosys.
Not used when coupling with nuopc-cmeps</desc>
</entry>

<entry id="HAMOCC_EXTNCYCLE">
Expand All @@ -163,7 +164,8 @@
</values>
<group>run_component_blom</group>
<file>env_run.xml</file>
<desc>Nitrogen deposition coupled from atmosphere. Requires module ecosys and extncycle</desc>
<desc>Nitrogen deposition coupled from atmosphere. Requires module ecosys and extncycle.
Not used when coupling with nuopc-cmeps</desc>
</entry>

<entry id="HAMOCC_N2OC">
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58 changes: 41 additions & 17 deletions cime_config/namelist_definition_blom.xml
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Original file line number Diff line number Diff line change
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>

<!-- ========================= -->
<!-- namelist group: vcoord -->
<!-- ========================= -->
Expand Down Expand Up @@ -3830,15 +3839,15 @@
<desc>File name (incl. full path) for atmopheric N-deposition data</desc>
</entry>

<entry id="do_ndep_coupled" modify_via_xml="HAMOCC_ATMNDEPC">
<entry id="use_nuopc_ndep">
<type>logical</type>
<category>bgcnml</category>
<group>bgcnml</group>
<category>config_bgc</category>
<group>config_bgc</group>
<values>
<value>.false.</value>
<value blom_n_deposition="yes" hamocc_atmndepc="yes" hamocc_extncycle="yes">.true.</value>
<value comp_interface="nuopc">.true.</value>
</values>
<desc>Switch to couple nitrogen deposition. Requires do_ndep.</desc>
<desc>if .true., use NUOPC to obtain NDEP (always imported to model).</desc>
</entry>

<entry id="do_n2onh3_coupled" modify_via_xml="HAMOCC_N2OC">
Expand Down Expand Up @@ -6051,7 +6060,7 @@
<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 +8747,21 @@
<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
57 changes: 28 additions & 29 deletions cime_config/ocn_in.readme
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,7 @@
! CWMI : Array of grid cell i-indices (i)
! CWMJ : Array of grid cell j-indices (i)
! CWMWTH : Array of modified grid cell widths (m) (f)
!
!
!===========================================================================
! NAMELIST FOR MERIDIONAL OVERTURNING AND FLUX DIAGNOSTICS
!
Expand All @@ -188,15 +188,15 @@
! for each region (i)
! MER_MINLAT : Minimum latitude to be considered for each region (f)
! MER_MAXLAT : Maximum latitude to be considered for each region (f)
!
!
!===========================================================================
! NAMELIST FOR SECTION TRANSPORT DIAGNOSTICS
!
! CONTENTS:
!
! SEC_SIFILE : Name of file containing section specification for section
! transport computation (a)
!
!
!===========================================================================
! IO-NAMELIST FOR DIAGNOSTIC OUTPUT
!
Expand Down Expand Up @@ -230,10 +230,10 @@
! MSC_ - miscellanous, non-gridded fields
!
! Global parameters:
! FNAMETAG - tag used in file name (c10)
! AVEPERIO - average period in days (i)
! FILEFREQ - how often to start a new file in days (i)
! COMPFLAG - switch for compressed/uncompressed output (i)
! FNAMETAG - tag used in file name (c10)
! AVEPERIO - average period in days (i)
! FILEFREQ - how often to start a new file in days (i)
! COMPFLAG - switch for compressed/uncompressed output (i)
! NCFORMAT - netcdf format (valid arguments are 0 for classic,
! 1 for 64-bit offset and 2 for netcdf4/hdf5 format)
!
Expand Down Expand Up @@ -380,13 +380,12 @@
!
! 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
! 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
! DO_NDEP_COUPLED: Logical to apply N-deposition fluxes received from the atmosphere (true=atm, false=clim), requires DO_NDEP=TRUE
! NDEPFILE : File name (incl. full path) for atmopheric N-deposition data
! NDEPFILE : File name (incl. full path) for atmopheric N-deposition data (not used for coupling to cmeps)
! DO_N2ONH3_COUPLED: Logical switch for interactive coupling of N2O and NH3 fluxes (true=atm, false=fix atmospheric value)
! DO_SEDSPINUP: Logical switch to activate sediment spin-up
! SEDSPIN_YR_S: Start year for sediment spinup
Expand All @@ -398,21 +397,21 @@
! PI_PH_FILE : File name (incl. full path) for surface PI pH input data.
! use_M4AGO : Switch for M4AGO settling scheme
! LEUPHOTIC_CYA : Switch to perform bluefix (cyanobacteria) only in the euphotic zone
! L_3DVARSEDPOR : Logical switch to enable lon-lat-depth variable sediment porosity (as opposed to default: only depth)
! L_3DVARSEDPOR : Logical switch to enable lon-lat-depth variable sediment porosity (as opposed to default: only depth)
! SEDPORFILE : File name (incl. full path) for sediment porosity
!
!===========================================================================
! NAMELIST BGCPARAMS FOR iHAMOCC-BGC PARAMETERS (DEVELOPERS ONLY)
!
!
! CONTENTS: EMPTY BY DEFAULT
! FOR ADJUSTABLE PARAMETERS, SEE CODE
!
!
!===========================================================================
! NAMELIST BGCOAFX FOR ALKALINIZATION SCENARIO
!
! CONTENTS:
!
! OALKSCEN : Name of alkalinization scenario ('const', 'ramp', or 'file')
! OALKSCEN : Name of alkalinization scenario ('const', 'ramp', or 'file')
! OALKFILE : Full path of the input file for the alkalinization scenario 'file'
! ADDALK : Pmol alkalinity/yr added in 'const' or 'ramp' scenarios
! CDRMIP_LATMAX : Max latitude where alkalinity is added in 'const' or 'ramp' scenarios
Expand All @@ -434,10 +433,10 @@
! BUR_ - 2d fields of sediment burial
!
! Global parameters:
! FNAMETAG - tag used in file name (c10)
! AVEPERIO - average period in days (i)
! FILEFREQ - how often to start a new file in days (i)
! COMPFLAG - switch for compressed/uncompressed output (i)
! FNAMETAG - tag used in file name (c10)
! AVEPERIO - average period in days (i)
! FILEFREQ - how often to start a new file in days (i)
! COMPFLAG - switch for compressed/uncompressed output (i)
! NCFORMAT - netcdf format (valid arguments are 0 for classic,
! 1 for 64-bit offset and 2 for netcdf4/hdf5 format)
! INVENTORY- how often to write an inventory of tracers to ocean
Expand Down Expand Up @@ -487,7 +486,7 @@
! PHOSY - Primary production (pp) [mol C m-3 s-1]
! CO3 - Carbonate ions (co3) [mol C m-3]
! N2O - Nitrous oxide concentration [mol N2O m-3]
! NITR_NH4 - nitrification rate on NH4 [mol NH4 m-3 s-1] - extended N cycle only
! NITR_NH4 - nitrification rate on NH4 [mol NH4 m-3 s-1] - extended N cycle only
! NITR_NO2 - nitrification rate on NO2 [mol NO2 m-3 s-1] - extended N cycle only
! NITR_N2O_PROD - N2O production rate during nitrification on NH4 [mol N2O m-3 s-1] - ext. N cycle only
! NITR_NH4_OM - detritus production during nitrification on NH4 [mol P m-3 s-1] - ext. N cycle only
Expand All @@ -498,9 +497,9 @@
! DNRA_NO2 - DNRA on NO2 [mol NO2 m-3 s-1] - ext. N cycle only
! ANMX_N2_PROD - anammox N2 production [mol N2 m-3 s-1] - ext. N cycle only
! ANMX_OM_PROD - anammox detritus production [mol P m-3 s-1] - ext. N cycle only
! PHOSY_NH4 - PP consumption of NH4 [mol NH4 m-3 s-1] - ext. N cycle only
! PHOSY_NO3 - PP consumption of NH4 [mol NH4 m-3 s-1] - ext. N cycle only
! REMIN_AEROB - aerob remineralization rate (sev. sources) [mol NH4 m-3 s-1] - ext. N cycle only
! PHOSY_NH4 - PP consumption of NH4 [mol NH4 m-3 s-1] - ext. N cycle only
! PHOSY_NO3 - PP consumption of NH4 [mol NH4 m-3 s-1] - ext. N cycle only
! REMIN_AEROB - aerob remineralization rate (sev. sources) [mol NH4 m-3 s-1] - ext. N cycle only
! REMIN_SULF - sulfate-based remin rate on det [mol P m-3 s-1] - ext. N cycle only
! AGG_WS - M4AGO aggregate mean settling velocity [m/d]
! DYNVIS - molecular dynamic viscosity of sea water [kg m-1 s-1]
Expand Down Expand Up @@ -549,8 +548,8 @@
! PCO2M - Surface PCO2 under moist air assumption [uatm]
! KWCO2 - Piston velocity (kwco2) [m s-1]
! KWCO2KHM - Piston velocity times solubility (kwco2*kh; moist air) [m s-1 mol kg-1 uatm-1]
! CO2KH - CO2 solubility under dry air assumption (khd) [mol kg-1 atm-1]
! CO2KHM - CO2 solubility under moist air assumption (kh) [mol kg-1 atm-1]
! CO2KH - CO2 solubility under dry air assumption (khd) [mol kg-1 atm-1]
! CO2KHM - CO2 solubility under moist air assumption (kh) [mol kg-1 atm-1]
! CO2FXD - Downward CO2 flux (co2fxd) [kg C m-2 s-1]
! CO2FXU - Upward CO2 flux (co2fxu) [kg C m-2 s-1]
! NIFLUX - Nitrogen flux (fgn2) [mol N2 m-2 s-1]
Expand Down Expand Up @@ -608,7 +607,7 @@
! BURSSSC12 - burial fluxes of calcium carbonate [mol Ca m-2 s-1]
! BURSSSSIL - burial fluxes of silicate [mol Si m-2 s-1]
! BURSSSTER - burial fluxes of clay [g m-2 s-1]
!
!
! Sediment fields (SDM)
! POWAIC - (powdic) [mol C m-3]
! POWAAL - (powalk) [eq m-3]
Expand All @@ -620,7 +619,7 @@
! POWNH4 - (pownh4) [mol NH4 m-3] - extended N cycle only
! POWN2O - (pown2o) [mol N2O m-3] - extended N cycle only
! POWNO2 - (powno2) [mol NO2 m-3] - extended N cycle only
! NITR_NH4 - nitrification rate on NH4 [mol NH4 m-3 s-1] - extended N cycle only
! NITR_NH4 - nitrification rate on NH4 [mol NH4 m-3 s-1] - extended N cycle only
! NITR_NO2 - nitrification rate on NO2 [mol NO2 m-3 s-1] - extended N cycle only
! NITR_N2O_PROD - N2O production rate during nitrification on NH4 [mol N2O m-3 s-1] - ext. N cycle only
! NITR_NH4_OM - detritus production during nitrification on NH4 [mol P m-3 s-1] - ext. N cycle only
Expand All @@ -631,9 +630,9 @@
! DNRA_NO2 - DNRA on NO2 [mol NO2 m-3 s-1] - ext. N cycle only
! ANMX_N2_PROD - anammox N2 production [mol N2 m-3 s-1] - ext. N cycle only
! ANMX_OM_PROD - anammox detritus production [mol P m-3 s-1] - ext. N cycle only
! PHOSY_NH4 - PP consumption of NH4 [mol NH4 m-3 s-1] - ext. N cycle only
! PHOSY_NO3 - PP consumption of NH4 [mol NH4 m-3 s-1] - ext. N cycle only
! REMIN_AEROB - aerob remineralization rate (sev. sources) [mol NH4 m-3 s-1] - ext. N cycle only
! PHOSY_NH4 - PP consumption of NH4 [mol NH4 m-3 s-1] - ext. N cycle only
! PHOSY_NO3 - PP consumption of NH4 [mol NH4 m-3 s-1] - ext. N cycle only
! REMIN_AEROB - aerob remineralization rate (sev. sources) [mol NH4 m-3 s-1] - ext. N cycle only
! REMIN_SULF - sulfate-based remin rate on det [mol P m-3 s-1] - ext. N cycle only
! SSSO12 - (ssso12) [mol m-3]
! SSSSIL - (ssssil) [mol Si m-3]
Expand Down
11 changes: 11 additions & 0 deletions drivers/nuopc/ocn_import_export.F90
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Original file line number Diff line number Diff line change
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
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