FATES-NOCOMP with Adrianna's SP calibration parameters

[rosiealice]

Purpose:
Like #10, except using Adrianna's calibrated values.

__
Description:

To get the code

git clone https://github.com/NorESMhub/NorESM.git
cd NorESM
git checkout noresm2_5_alpha08d
./bin/git-fleximod update
cd components/clm/src/fates
remote add adrianna_fates https://github.com/adrifoster/fates/
git fetch adrianna_fates
git checkout adrianna_fates/leaf_photo_update
cd ../
git fetch
git checkout ctsm5.3.11-noresm_v0

• NOTE: a memory leak is present in the run.
  See memory leak in n1850 case NorESM#550

• create_newcase commnad

./create_newcase --case i1850.FATES-NOCOMP-FAST.ne30_tn14.alpha08d_psupdate_calparams.20250108b
--compset 1850_DATM%QIA_CLM60%FATES_SICE_SOCN_MOSART_SGLC_SWAV 
--res ne30pg3_tn14 
--project NN9188K 
--run-unsupported 
--mach betzy


- **user_nl_clm**
use_fates_nocomp=TRUE
use_fates_fixed_biogeog=TRUE


fates_paramfile='/cluster/work/users/rosief/git/calibration_parameter_files/SP_calib/fates_params_psupdate_branch_5.3.10_AFupdates.nc'

hist_fexcl1 =
	      'FATES_VEGC_PF',
              'FATES_STOREC_PF', 'FATES_RECRUITMENT_PF', 'FATES_MORTALITY_PF', 'FATES_PATCHAREA_AP', 'FATES_LAI_AP',
              'FATES_CANOPYAREA_AP', 'FATES_NESTEROV_INDEX', 'FATES_IGNITIONS', 'FATES_FDI', 'FATES_ROS', 'FATES_EFFECT_WSPEED',
              'FATES_FUELCONSUMED', 'FATES_FIRE_INTENSITY', 'FATES_FIRE_INTENSITY_BURNFRAC', 'FATES_BURNFRAC', 'FATES_FUEL_MEF',
              'FATES_FUEL_BULKD', 'FATES_FUEL_EFF_MOIST', 'FATES_FUEL_SAV', 'FATES_FUEL_AMOUNT', 'FATES_FRAGMENTATION_SCALER_SL',
              'FATES_FUEL_MOISTURE_FC', 'FATES_FUEL_AMOUNT_FC', 'FATES_BURNFRAC_AP', 'FATES_FIRE_INTENSITY_BURNFRAC_AP',
              'FATES_FUEL_AMOUNT_AP', 'FATES_FUEL_BURNT_BURNFRAC_FC',
	      'FATES_LITTER_IN_EL', 'FATES_LITTER_OUT_EL', 'FATES_SEED_BANK_EL', 'FATES_SEEDS_IN_LOCAL_EL',
              'FATES_SEEDS_IN_EXTERN_EL', 'FATES_SEED_GERM_EL', 'FATES_SEED_DECAY_EL', 'FATES_STOREC', 'FATES_VEGC',
              'FATES_SAPWOODC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 
              'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
              'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
              'FATES_HARVEST_WOODPROD_C_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY',
              'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY', 'FATES_CROWNAREA_CL', 'FATES_DEMOTION_CARBONFLUX',
              'FATES_PROMOTION_CARBONFLUX', 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_USTORY', 
              'FATES_DDBH_CANOPY_SZ', 'FATES_DDBH_USTORY_SZ', 'FATES_BASALAREA_SZ',
              'FATES_VEGC_ABOVEGROUND_SZ', 'FATES_LAI_CANOPY_SZ', 'FATES_MORTALITY_CANOPY_SZ', 'FATES_NPLANT_USTORY_SZ',
              'FATES_LAI_USTORY_SZ', 'FATES_NPLANT_SZ', 'FATES_NPLANT_AC', 'FATES_MORTALITY_BACKGROUND_SZ',
              'FATES_MORTALITY_HYDRAULIC_SZ', 'FATES_MORTALITY_CSTARV_SZ', 'FATES_MORTALITY_IMPACT_SZ',
              'FATES_MORTALITY_FIRE_SZ', 'FATES_MORTALITY_TERMINATION_SZ', 'FATES_MORTALITY_LOGGING_SZ',
              'FATES_MORTALITY_FREEZING_SZ', 'FATES_MORTALITY_SENESCENCE_SZ', 'FATES_MORTALITY_AGESCEN_SZ',
              'FATES_MORTALITY_AGESCEN_AC', 'FATES_MORTALITY_USTORY_SZ', 'FATES_FROOTMAINTAR', 'FATES_CROOTMAINTAR',
              'FATES_LSTEMMAINTAR', 'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL',
              'FATES_LITTER_AG_FINE_EL', 'FATES_LITTER_BG_FINE_EL', 'FATES_LITTER_BG_CWD_EL', 'FATES_LITTER_AG_CWD_EL',
              'FATES_LITTER_CWD_ELDC',
'FATES_NPP_PF','FATES_MORTALITY_LOGGING_SE_SZ',
'FATES_MORTALITY_HYDRAULIC_SE_SZ','FATES_MORTALITY_FREEZING_SE_SZ',
'FATES_MORTALITY_CSTARV_SE_SZ','FATES_MORTALITY_CANOPY_SE_SZ',
'FATES_MORTALITY_CANOPY_SE_SZ','FATES_MORTALITY_BACKGROUND_SE_SZ',
'FATES_MORTALITY_BACKGROUND_SE_SZ','FATES_MORTALITY_AGESCEN_SE_SZ',
'FATES_VEGC_SE_PF','FATES_RECRUITMENT_CFLUX_PF','FATES_NPP_SE_PF',
'FATES_NPP_SE_PF','FATES_NPLANT_SEC_PF','FATES_NOCOMP_PATCHAREA_PF',
'FATES_NOCOMP_NPATCHES_PF','FATES_NOCOMP_BURNEDAREA_PF',
'FATES_MORT_CSTARV_CONT_CFLUX_PF','FATES_MORTALITY_HYDRO_CFLUX_PF',
'FATES_MORTALITY_FIRE_CFLUX_PF','FATES_MORTALITY_CSTARV_CFLUX_PF',
'FATES_MORTALITY_CFLUX_PF','FATES_MEANSMP_DROUGHTPHEN_PF',
'FATES_MEANLIQVOL_DROUGHTPHEN_PF','FATES_LEAFC_PF',
'FATES_L2FR_USTORY_REC_PF','FATES_L2FR_CANOPY_REC_PF',
'FATES_GPP_SE_PF','FATES_ELONG_FACTOR_PF','FATES_DROUGHT_STATUS_PF',
'FATES_DAYSINCE_DROUGHTLEAFON_PF','FATES_DAYSINCE_DROUGHTLEAFOFF_PF',
'FATES_CANOPYCROWNAREA_PF','FATES_TRANSITION_MATRIX_LULU',
'FATES_DISTURBANCE_RATE_MATRIX_LULU','FATES_PATCHAREA_LU'

• xmlchange commands

./xmlchange STOP_OPTION=nyears
./xmlchange STOP_N=2
./xmlchange RESUBNIT=20


**Compset long name**
1850_DATM%QIA_CLM60%FATES_SICE_SOCN_MOSART_SGLC_SWAV
___
**Model grid long name**
`a%ne30np4.pg3_l%ne30pg4.pg3_oi%tnx1v4_r%r05_w%null_z%null_g%gris4_m%tnx1v4`

**Case directory:**
- Locally on betzy: 
   `/cluster/work/users/rosief/git/noresm2_5_alpha08d_psbranch/cime/scripts/ i1850.FATES-NOCOMP-FAST.ne30_tn14.alpha08d_psupdate_calparams.20250108b

- On github:
tbd
___
**Code version on github (either NorESMhub or user's fork):**
(see checkout instructions) 
___
**Diagnostics:**
- Diags (if available):

___
**Output:**
- Raw output on nird (if still available): 
/datalake/NS9560K/noresm3/cases/ i1850.FATES-NOCOMP-FAST.ne30_tn14.alpha08d_psupdate_calparams.20250108b/lnd/hist/ 
___
**Contacts:**
@rosiealice 
___
**Extra details:**

[kjetilaas]

Hi @rosiealice! I as able to run this on betzy. I have only competed 10 yrs, but it already shows signs of quite large areas dying, especially in the Amazone and boreal regions.

From what I can see, this seems to come from carbon starvation in both locations (left column is a grid-point in the Amazon, 3. column is in the boreal zone):

[kjetilaas]

Link to folder on NIRD:
/nird/datalake/NS9560K/kjetisaa/i1850.FATES-NOCOMP.ne30pg3_tn14.alpha08d.20250218_coldstart_adrianas_tuning

And diagnostics:
https://ns9560k.web.sigma2.no/datalake/diagnostics/noresm/kjetisaa/i1850.FATES-NOCOMP.ne30pg3_tn14.alpha08d.20250218_coldstart_adrianas_tuning/

[kjetilaas]

FTR, here are the steps I use to create the case:

    noresmrepo="NorESM_alpha08d_photosynthesis_update" 
    git clone https://github.com/NorESMhub/NorESM/ $noresmrepo #If this is crashing, try loging in to another node, e.g.: ssh -Y brukernavn@login-3.betzy.sigma2.no        
    cd $noresmrepo
    git checkout noresm2_5_alpha08d

    echo "updating externals"
    ./bin/git-fleximod update

    cd componensts/clm/src
    git fetch origin
    git checkout ctsm5.3.11-noresm_v0

    cd fates
    git remote add afoster https://github.com/adrifoster/fates.git
    git fetch afoster
    git checkout leaf_photo_update

   cd /cluster/work/users/$USER/$noresmrepo/cime/scripts/
   ./create_newcase --case /cluster/work/users/kjetisaa/i1850.FATES-NOCOMP.ne30pg3_tn14.alpha08d.20250218_coldstart_adrianas_tuning --compset 1850_DATM%QIA_CLM60%FATES_SICE_SOCN_SROF_SGLC_SWAV --res ne30pg3_tn14 --project nn9560k --run-unsupported --mach betzy -pecount L

[rosiealice]

This is great! Both in terms of getting this case to run and also with the diagnostics. Do we have a matching FATES-SP case so we can check out whether the GPP is Ok with the right LAI (and therefore concentrate on the carbon economy parameters).