NOCOMP run with Adrianna's photosynthesis updates branch

[rosiealice]

Purpose:
To check whether we can make the branch with the photosthesis update run in a NorESM configuration.

n.b. that to run this requires pulling back to an earlier branch of CTSM without the changes to MEGAN which cause conlflicts with this code (we can resolve these, but have not done so yet).
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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.20250108 --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/noresm2_5_alpha08d_psbranch/components/clm/src/fates/parameter_files/fates_params_default_medlyn.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
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**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.20250108 

- On github:
tbd
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**Code version on github (either NorESMhub or user's fork):**
- On github:  https://github.com/NorESMhub/NorESM/releases/tag/noresm2_5_alpha08d
- https://github.com/username/noresm/tree/<code_version>
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**Diagnostics:**
- Diags (if available):

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**Output:**
- Raw output on nird (if still available): 
/datalake/NS9560K/noresm3/cases/ i1850.FATES-NOCOMP-FAST.ne30_tn14.alpha08d_psupdate.20250108/lnd/hist/ 
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**Contacts:**
@rosiealice 
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**Extra details:**