CTSM 5.3 Spinup and HIST on f09 grid (2nd Attempt - with li2024crujra fire ON this time and using filled Antarctica datm data)

[olyson]

Description:
Same as #68, but on f09 grid This will include a full historical run so we also get restarts (initial files) in 1979 and 2000 for B or F2000 cases.

---

Case directory:
Locally:
/glade/work/oleson/ctsm5.3.n04_ctsm5.2.028/cime/scripts/ctsm53n04ctsm52028_f09_AD
/glade/work/oleson/ctsm5.3.n04_ctsm5.2.028/cime/scripts/ctsm53n04ctsm52028_f09_SASU
/glade/work/oleson/ctsm5.3.n04_ctsm5.2.028/cime/scripts/ctsm53n04ctsm52028_f09_pSASU
/glade/work/oleson/ctsm5.3.n04_ctsm5.2.028/cime/scripts/ctsm53n04ctsm52028_f09_hist

---

Sandbox:
Locally:
/glade/work/oleson/ctsm5.3.n04_ctsm5.2.028
git describe: branch_tags/ctsm5.3.n04_ctsm5.2.028

---

user_nl_ changes:

****user_nl_clm:

AD

hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', 'TOTSOMN', 'TOTVEGC', 'TOTVEGN', 'TLAI', 'GPP', 'CPOOL', 'NPP', 'TWS','H2OSNO'

! turn off shifting cultivation
do_grossunrep = .false.

! do this for isotopes
use_c13 = .true.
use_c14 = .true.
use_c13_timeseries = .true.
use_c14_bombspike = .true.

SASU

finidat = '/glade/campaign/cgd/tss/people/oleson/CLM5_restarts/ctsm53n04ctsm52028_f09_AD.clm2.r.0281-01-01-00000.nc'
reseed_dead_plants = .true.

hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', 'TOTSOMN', 'TOTVEGC', 'TOTVEGN', 'TLAI', 'GPP', 'CPOOL', 'NPP', 'TWS','H2OSNO'

! turn off shifting cultivation
do_grossunrep = .false.

! do this for isotopes
use_c13 = .true.
use_c14 = .true.
use_c13_timeseries = .true.
use_c14_bombspike = .true.

pSASU

finidat = '/glade/campaign/cgd/tss/people/oleson/CLM5_restarts/ctsm53n04ctsm52028_f09_SASU.clm2.r.0281-01-01-00000.nc'

reseed_dead_plants = .true.

! turn off shifting cultivation
do_grossunrep = .false.

! do this for isotopes
use_c13 = .true.
use_c14 = .true.
use_c13_timeseries = .true.
use_c14_bombspike = .true.

hist

finidat = '/glade/campaign/cgd/tss/people/oleson/CLM5_restarts/ctsm53n04ctsm52028_f09_pSASU.clm2.r.0161-01-01-00000.nc'

! turn off shifting cultivation
do_grossunrep = .false.

ndep_taxmode = 'extend'

hist_fincl1 += 'FSDSND','FSDSVD','FSDSNI','FSDSVI','RAIN_FROM_ATM','SNOW_FROM_ATM','FLDS_NOT_DOWNSCALED','ZBOT','Tair_from_atm','Thair_from_atm','QBOT_NOT_DOWNSCALED','PBOT_NOT_DOWNSCALED','Rho_from_atm','PCO2','UWIND','VWIND','BCPHIDRY','BCPHODRY','BCPHIWET','OCPHIDRY','OCPHODRY','OCPHIWET','DSTWET1','DSTDRY1','DSTWET2','DSTDRY2','DSTWET3','DSTDRY3','DSTWET4','DSTDRY4','ATM_TOPO'

use_init_interp = .true.

! Generated from ./create_newcase ..... --user-mods-dir output_crop_highfreq and edited for only h0,h1,h2,h3,h4

!----------------------------------------------------------------------------------
! Settings from output_base
!----------------------------------------------------------------------------------

! h0 stream (monthly average, gridcell-level)
! h0 stream ICE variables and other variables inactive by default (monthly average, gridcell-level)
! Emon, Lmon, LIMon
hist_mfilt(1) = 1
hist_dov2xy(1) = .true.
hist_nhtfrq(1) = 0
hist_type1d_pertape(1) = ' '
!hist_fexcl1 += 'PCT_GLC_MEC','PCT_NAT_PFT'
hist_fexcl1 += 'PCT_GLC_MEC'
hist_fincl1 += 'EFLX_LH_TOT_ICE', 'FIRE_ICE', 'FLDS_ICE', 'FSH_ICE', 'FSNO_ICE', 'FSR_ICE', 'QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE', 'QRUNOFF_ICE', 'QSNOFRZ_ICE', 'QSNOMELT_ICE', 'RAIN_ICE', 'SNOW_ICE', 'SNOWICE_ICE', 'SNOWLIQ_ICE', 'SNOTXMASS_ICE', 'TG_ICE', 'TOPO_COL_ICE', 'TSA_ICE', 'TSOI_ICE'

! h1 stream (monthly average, finest sub-grid)
! Emon, Lmon
hist_mfilt(2) = 1
hist_dov2xy(2) = .false.
hist_nhtfrq(2) = 0
hist_type1d_pertape(2) = ' '
hist_fincl2 += 'TLAI', 'TSA','TREFMNAV','TREFMXAV', 'BTRANMN', 'Vcmx25Z', 'FSH', 'VEGWP', 'FCTR', 'FCEV', 'FGEV', 'FIRE', 'FSR', 'FIRA', 'FSA', 'GSSUNLN', 'GSSHALN', 'TSKIN'

! h2 stream (monthly average, landunit-level)
! Emon
hist_mfilt(3) = 1
hist_dov2xy(3) = .false.
hist_nhtfrq(3) = 0
hist_type1d_pertape(3) = 'LAND'
hist_fincl3 += 'FSR', 'H2OSNO', 'Q2M', 'SNOWDP', 'TSA', 'TREFMNAV', 'TREFMXAV', 'TG', 'QRUNOFF', 'FSH', 'FIRE', 'FIRA', 'FGR', 'EFLX_LH_TOT', 'RH2M', 'TLAI', 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'U10', 'TSOI_10CM', 'QIRRIG_DRIP', 'URBAN_HEAT', 'WASTEHEAT', 'TSKIN'
! h2 stream (monthly average, landunit-level)
! Emon
hist_mfilt(3) = 1
hist_dov2xy(3) = .false.
hist_nhtfrq(3) = 0
hist_type1d_pertape(3) = 'LAND'
hist_fincl3 += 'FSR', 'H2OSNO', 'Q2M', 'SNOWDP', 'TSA', 'TREFMNAV', 'TREFMXAV', 'TG', 'QRUNOFF', 'FSH', 'FIRE', 'FIRA', 'FGR', 'EFLX_LH_TOT', 'RH2M', 'TLAI', 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'U10', 'TSOI_10CM', 'QIRRIG_DRIP', 'URBAN_HEAT', 'WASTEHEAT', 'TSKIN'

! h3 stream (yearly average, gridcell-level)
! Eyr
hist_mfilt(4) = 1
hist_dov2xy(4) = .true.
hist_nhtfrq(4) = -8760
hist_type1d_pertape(4) = ' '
hist_fincl4 += 'PCT_GLC_MEC', 'QICE_FORC', 'TSRF_FORC', 'TOPO_FORC', 'PCT_NAT_PFT','PCT_LANDUNIT','FSNO_ICE'

! h4 stream (yearly average, landunit-level)
! Eyr landuse tiles
! (No fields in base, but other usermods add to this stream)
hist_mfilt(5) = 1
hist_dov2xy(5) = .false.
hist_nhtfrq(5) = -8760
hist_type1d_pertape(5) = 'LAND'

!----------------------------------------------------------------------------------
! Settings from cmip6_carbon_isotopes
! CAN ONLY USE THIS IF STARTING FROM AN INITIAL FILE THAT HAS ISOTOPES
!----------------------------------------------------------------------------------

use_c13 = .true.
use_c14 = .true.
use_c13_timeseries = .true.
use_c14_bombspike = .true.

! h0 stream (monthly average, gridcell-level)
hist_fexcl1 += 'C14_SOILC_vr'

! h3 stream (yearly average, gridcell-level)
hist_fincl4 += 'C14_SOILC_vr'

!----------------------------------------------------------------------------------
! Settings from output_bgc
!----------------------------------------------------------------------------------

! h0 stream (monthly average, gridcell-level)
hist_fexcl1 += 'SOM_ACT_C_vr', 'SOM_ACT_N_vr', 'SOM_SLO_C_vr', 'SOM_SLO_N_vr', 'SOM_PAS_C_vr', 'SOM_PAS_N_vr', 'SOILC_vr', 'SOILN_vr', 'CWD_C_vr', 'LIT_MET_C_vr', 'LIT_CEL_C_vr', 'LIT_LIG_C_vr', 'LIT_MET_N_vr', 'LIT_CEL_N_vr', 'LIT_LIG_C_vr', 'CWD_N_vr', 'SMIN_NO3_vr', 'CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr'
hist_fincl1 += 'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','LIT_MET_C_TO_SOM_ACT_C','LIT_MET_N_TO_SOM_ACT_N','LIT_CEL_C_TO_SOM_ACT_C', 'LIT_CEL_N_TO_SOM_ACT_N','LIT_LIG_C_TO_SOM_SLO_C','LIT_LIG_N_TO_SOM_SLO_N','DWT_WOOD_PRODUCTC_GAIN_PATCH'

! h1 stream (monthly average, finest sub-grid)
hist_fincl2 += 'GPP', 'NPP', 'AGNPP', 'TOTVEGC', 'NPP_NUPTAKE', 'AR', 'HR', 'HTOP'

! h2 stream (monthly average, landunit-level)
! TOT_WOODPRODC:I, CROPPROD1C:I, and NEE are not available at the landunit level
hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'SLASH_HARVESTC', 'COL_FIRE_CLOSS', 'DWT_SLASH_CFLUX_PATCH', 'FROOTC:I', 'HTOP'

! h3 stream (yearly average, gridcell-level)
hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWD_C_vr', 'LIT_MET_C_vr', 'LIT_CEL_C_vr', 'LIT_LIG_C_vr', 'LIT_MET_N_vr', 'LIT_CEL_N_vr', 'LIT_LIG_N_vr','CWD_N_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I'

! h4 stream (yearly average, landunit-level)
hist_fincl5 += 'TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I', 'FROOTC:I'

!----------------------------------------------------------------------------------
! Settings from output_crop
!----------------------------------------------------------------------------------

! h0 stream (monthly average, gridcell-level)
hist_fexcl1 += 'PCT_CFT'

! h1 stream (monthly average, finest sub-grid)
hist_fincl2 += 'GRAINC_TO_FOOD','NFERTILIZATION'

! h2 stream (monthly average, landunit-level)
hist_fincl3 += 'GRAINC_TO_FOOD'

! h3 stream (yearly average, gridcell-level)
hist_fincl4 += 'PCT_CFT','CROPPROD1C:I'

user_nl_datm_streams:

CLMCRUNCEPv7.Solar:datafiles=/glade/derecho/scratch/wwieder/TRENDY2024/inputs/three_stream/clmforc.CRUJRAv2.5_0.5x0.5.Solr.1901.nc, ...through 2023
CLMCRUNCEPv7.Solar:meshfile=/glade/derecho/scratch/slevis/temp_work/TRENDY2024/inputs/three_stream/mesh_cdf5.nc
CLMCRUNCEPv7.Solar:datavars= FSDS Faxa_swdn

CLMCRUNCEPv7.Precip:datafiles=/glade/derecho/scratch/wwieder/TRENDY2024/inputs/three_stream/clmforc.CRUJRAv2.5_0.5x0.5.Prec.1901.nc, ...through 2023
CLMCRUNCEPv7.Precip:meshfile=/glade/derecho/scratch/slevis/temp_work/TRENDY2024/inputs/three_stream/mesh_cdf5.nc

CLMCRUNCEPv7.TPQW:datafiles=/glade/derecho/scratch/wwieder/TRENDY2024/inputs/three_stream/clmforc.CRUJRAv2.5_0.5x0.5.TPQWL.1901.nc, ...through 2023
CLMCRUNCEPv7.TPQW:meshfile=/glade/derecho/scratch/slevis/temp_work/TRENDY2024/inputs/three_stream/mesh_cdf5.nc
CLMCRUNCEPv7.TPQW:datavars = QBOT Sa_shum,PSRF Sa_pbot,TBOT Sa_tbot,WIND Sa_wind,FLDS Faxa_lwdn

---

SourceMods:
NONE

---

Diagnostics:
Preliminary look at the last 20 years of pSASU (101-120) compared to Issue #65 . The main difference between these two simulations is the new fire model:
https://webext.cgd.ucar.edu/I1850/ctsm53n04ctsm52028_f09_pSASU/lnd/ctsm53n04ctsm52028_f09_pSASU_101_120-ctsm52026_f09_pSASU_401_420/setsIndex.html

ILAMB diagnostics for the historical:
https://webext.cgd.ucar.edu/I20TR/ctsm53n04ctsm52028_f09_hist/lnd/_build_ctsm53n04ctsm52028_f09_hist/
Standard diagnostics:
https://webext.cgd.ucar.edu/I20TR/ctsm53n04ctsm52028_f09_hist/lnd/ctsm53n04ctsm52028_f09_hist_2004_2023-ctsm52026_f09_hist_2004_2023/setsIndex.html
Comparison to #67 is here

---

Output:
Output (if still available):
/glade/scratch/oleson/archive/ctsm53n04ctsm52028_f09_AD
/glade/scratch/oleson/archive/ctsm53n04ctsm52028_f09_SASU
/glade/scratch/oleson/archive/ctsm53n04ctsm52028_f09_pSASU
/glade/campaign/cgd/tss/common/Land_Only_Simulations/CTSM53_DEV/ctsm53n04ctsm52028_f09_hist

---

Contacts:
@olyson

---

Extra details:

AD: 280 yrs, 2.37% disequilibrium
SASU: 280 yrs, 12.74% disequilibrium
pSASU: 160 yrs, 2.55% disequilibrium
hist: complete, 1850-2023

[olyson]

Preliminary look at the last 20 years of pSASU (101-120) compared to #65 . The main difference between these two simulations is the new fire model:
https://webext.cgd.ucar.edu/I1850/ctsm53n04ctsm52028_f09_pSASU/lnd/ctsm53n04ctsm52028_f09_pSASU_101_120-ctsm52026_f09_pSASU_401_420/setsIndex.html

I see mostly decreases in TLAI, which generally seem to correspond to increased fire.

[wwieder]

Thanks for plotting these up, Keith. Would it be helpful to discuss these further? Have you already started historical runs? I'm curious what PFT max LAIs look like with the fire on, but maybe we can just look at these at the end of the historical run?

[olyson]

I have not started historicals. I could branch the f09 1850 pSASU and output pft-level data. Might be a good idea to look at that first.

[wwieder]

Note, I'll create new datasets with 1921-2022 datm data that have merged CRUJRA - GSWP3 to get data for Antarctica.

[olyson]

Survivability and max TLAI plots for last year of pSASU. Deciduous tropical tree looks more under control than in #65 . C4 grass stills looks a bit problematic with lower LAI than in #65 and similar survivability .

[wwieder]

Thanks @olyson. Lack of C3 and C4 grasses in savannah regions seems like a concern. Seems hard to untangle this from the fire and parameterizations suggested by @lifang0209 + all the other changes that came in with the 5.3 tag. Hopefully @linniahawkins and the PPE can bring back the grass 🌱 (I know it's a dicot seedling, but 🌽 also seemed misleading)

[wwieder]

FWIW, soils around savannah regions a bit drier with the updated parameter sets, but what really stands out is how much more water stressed tropical forests are here comparing #65 (with new 'hand tuned-PPE informed' parameter file) to #62, with the older GSWP3 tuned file. Is this what you'd expect @djk2120?
.

Maybe this warrant creating a new discussion thread, here or in PPE docs?

[lifang0209]

@olyson @wwieder @samsrabin Hi Keith, have you run CTSM5.3's historical case with new fire model and parameters, either forced by GSWP or CRUJRA？ If so, could you please provide me with the case and output directory paths? I could compare them with the present-day burned area observations and see if I need to tune fsr_pft down to decrease the burning of C4 grass.

[wwieder]

@olyson when you're back next week can you try using the new CRUJRA-GSWP3 data from 1901-2023 that now here /glade/derecho/scratch/wwieder/TRENDY2024/inputs/three_stream/