Update the What's New ctsm5.4 file

WhatsNewInCTSM5.4.md

@@ -1,4 +1,4 @@
-# What's new in CTSM 5.4 (tag `ctsm5.4.0xx`)
+# What's new in CTSM 5.4 (tag `ctsm5.4.002`)
 
 # Purpose and description of changes since CTSM 5.3 (tag `ctsm5.3.021`)
 
@@ -37,21 +37,23 @@ Changes to defaults for \`clm6\` physics:
 * See “Changes to FATES and the FATES parameter file” below.  
 * Namelist defaults change so that  
   * use\_c13/use\_c14 are on only for HistClm60Bgc compsets with CRUJRA2024 or CAM7 forcing; examples of when use\_c13/use\_c14 are now off include SSP and single-point compsets, as well as cases using older forcings, such as CAM6, GSWP3v1, Qian, and CRUv7  
-  * when use\_c13 or use\_c14 is on, turn on the corresponding time series file  
+  * when use\_c13 or use\_c14 is on, turn on the corresponding time series file  (responding to the CLM_CMIP_ERA flag)
+  * C13/C14 CMIP7 data is done using streams with new namelist variables (stream_*_atm_c13, stream_*_atm_c14)
   * irrigation is on for transient cases (1850-2000, 1850-2100, but not for clm4\_5).
 
 Changes for all physics versions:
 
 * Parameters updated: Added MIMICS parameter \`mimics\_fi\` (fraction of litter inputs that bypass litter pools, directly contributing to SOM) and updated other MIMICS parameters (https://github.com/ESCOMP/CTSM/pull/2365) to remove NPP control on turnover, fix density dependent control on turnover, add litterfall fluxes that bypass litter pools and contribute directly to soil organic matter.  
 * FATES parameter file updated: ([PR \#2965](https://github.com/ESCOMP/CTSM/pull/2965), [PR \#2904](https://github.com/ESCOMP/CTSM/pull/2904), [PR \#1344](https://github.com/NGEET/fates/pull/1344), [PR \#3087](https://github.com/ESCOMP/CTSM/pull/3087)). See “FATES parameter file” section below for details.  
 * New surface datasets and landuse timeseries files (see “surface datasets” section below).
+* CMIP7 C13/C14 atmospheric timeseries data
 
 ## Heads up
 
 * History tapes now split into two files from hX to hXi and hXa, where X is the tape number (e.g. h0i/h0a) and where "i" stands for history file containing instantaneous fields, while "a" stands for history file containing non-instantaneous fields. Details in the “history files” section below and in the PRs https://github.com/ESCOMP/ctsm/pull/2445 https://github.com/ESCOMP/MOSART/pull/117 https://github.com/ESCOMP/RTM/pull/61 and the corresponding issues.  
 * Adding time to 1d weighting fields in transient simulations PR https://github.com/ESCOMP/CTSM/pull/3328  
 * Regarding CMIP7 vs. CMIP6 inputs:  
-  * We supply only CMIP7 C13/C14 isotope datasets, so these get used regardless of CLM\_CMIP\_ERA setting.  
+  * C13/C14 isotope datasets are the new CMIP7 datasets using streams, when CLM_CMIP_ERA==cmip6, the older cmip6 files are used
   * We supply only CMIP7 population density with clm6 physics in non-SSP cases, because the fire model is calibrated to that; conversely, we supply only CMIP6 population density for pre-clm6 physics and for SSP cases.  
   * We supply only CESM2 nitrogen deposition (ndep), so this gets used regardless of CLM\_CMIP\_ERA setting.  
   * For DATM we supply only CMIP6 aerosols.  
@@ -147,4 +149,3 @@ The former is calculated as a function of the latter and can be time-evolving de
 * ne30 with \`Clm60BgcCropCruJra\`: https://github.com/NCAR/LMWG_dev/issues/123 (123\_HIST\_popDens)  
 * ne30 SP https://github.com/NCAR/LMWG_dev/issues/126  
 * f09 SP https://github.com/NCAR/LMWG_dev/issues/127
-

bld/namelist_files/namelist_definition_ctsm.xml

@@ -220,6 +220,7 @@ Index of rooting profile for soil carbon
 
 Changes rooting profile from Zeng 2001 double exponential (0) to
 Jackson 1996 single exponential (1) to Koven uniform exponential (2).
+(REMOVE, NOT in the CODE)
 </entry>
 
 <entry id="rooting_profile_varindex_water" type="integer" category="clm_physics"
@@ -1215,6 +1216,8 @@ number of segments per clump for decomposition
 <entry id="pertlim" type="real" category="clm_physics"
        group="clm_inparm" valid_values="" >
 Perturbation limit when doing error growth test
+(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)
+(deprecated -- will be removed)
 </entry>
 
 <entry id="rest_flag" type="logical" category="clm_restart"
@@ -1237,7 +1240,8 @@ If TRUE, use explicit, time-varying AC adoption rate for air-conditioning flux a
 
 <entry id="urban_traffic" type="logical" category="clm_physics"
        group="clmu_inparm" valid_values="" >
-If TRUE, urban traffic flux will be activated (Currently NOT implemented).
+If TRUE, urban traffic flux will be activated
+(Currently NOT implemented).
 </entry>
 
 <entry id="building_temp_method" type="integer" category="clm_physics"
@@ -1363,6 +1367,7 @@ CLM Biogeochemistry mode : Carbon Nitrogen model (CN)
        group="clm_inparm" valid_values="" value=".false.">
 CLM Biogeochemistry mode : Carbon Nitrogen with Dynamic Global Vegetation Model (CNDV)
 (or CLM45BGCDV if phys=clm4_5, vsoilc_centbgc='on', and clm4me='on')
+(deprecated -- will be removed)
 </entry>
 
 <entry id="use_fun" type="logical" category="bgc"
@@ -1404,6 +1409,7 @@ Toggle to use 25 lake layers instead of 10
        group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the VIC hydrologic parameterizations
 (vichydro=".true." is EXPERIMENTAL, UNSUPPORTED!)
+(deprecated -- will be removed)
 </entry>
 
 <entry id="use_crop" type="logical" category="physics"
@@ -2546,6 +2552,7 @@ If TRUE, add extra diagnostics for methane model to the history files
 Profile over which to distribute C and N coming from surface pools (leaves, stem, grain).
 </entry>
 
+
 <!-- some N cycle flags  -->
 <entry id="no_frozen_nitrif_denitrif" type="logical" category="clm_vertcn"
        group="clm_inparm" valid_values="" >
@@ -2755,6 +2762,7 @@ If TRUE, turn on methane biogeochemistry model for lake columns, using a simplif
 <entry id="usephfact" type="logical" category="clm_methane"
        group="ch4par_in" valid_values="" >
 If TRUE, apply a limitation to methane production based on the soil pH dataset.
+(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)
 </entry>
 
 <entry id="vmax_oxid_unsat" type="real" category="clm_methane"

doc/IMPORTANT_NOTES.md

@@ -0,0 +1,87 @@
+# Important Notes on Experimental Features of CTSM
+
+Namelist items that are not regularly tested or used. Some aren't even implemented.
+
+    See
+
+    '../bld/namelist_files/namelist_definition_ctsm.xml' -- for definitions of all namelist variables
+
+## CTSM experimental namelist items
+
+    The following are tested but not on by default (for any physics)
+
+    - all_active
+    - allow_invalid_gdd20_season_inputs
+    - h2osfcflag (deprecated)
+    - use_nvmovement
+    - use_soil_moisture_streams
+
+   The following are NOT currently tested nor turned on by default:
+
+    - allowlakeprod
+    - allow_invalid_swindow_inputs
+    - carbon_resp_opt
+    - ch4offline
+    - CN_evergreen_phenology_opt
+    - CNratio_floating
+    - do_sno_oc
+    - finundation_method = h2osfc
+    - maxpatch_glc /= 10
+    - megan_use_gamma_sm
+    - no_frozen_nitrif_denitrif
+    - overburden_compress_tfactor
+    - override_bgc_restart_mismatch_dump
+    - perchroot
+    - perchroot_alt
+    - pertlim (deprecated)
+    - reduce_dayl_factor (not implemented, it's commented out in the code)
+    - replenishlakec
+    - rooting_profile_method_soilcarbon (DELETE)
+    - rooting_profile_varindex_carbon /= 2
+    - rooting_profile_varindex_water /= 1
+    - snicar_dust_optics /= sahara
+    - snicar_numrad_snw /= 5
+    - snicar_snobc_intmix /= TRUE
+    - snicar_snodst_intmix /= TRUE
+    - snicar_snw_shape /= hexagonal_plate
+    - snicar_solarspec /= mid_latitude_winter
+    - snicar_use_aerosol /= FALSE
+    - urban_traffic (not implemented)
+    - use_cndv (deprecated)
+    - use_extralakelayers
+    - usefrootc
+    - usephfact
+    - use_vichydro (deprecated)
+    - vcmax_opt = 4
+
+## FATES experimental namelist items
+
+    FATES is a relatively new subcomponent of CTSM
+    Almost all FATES options include "fates" in the name
+
+    The following are tested, but not turned on by default:
+
+   - fates_seeddisp_cadence > 0
+   - fates_parteh_mode > 1
+   - use_fates_planthydro
+   - use_fates_managed_fire
+   - use_fates_tree_damage
+   - use_fates_cohort_age_tracking
+   - use_fates_lupft
+   - use_fates_potentialveg
+   - use_fates_ed_st3
+
+   The following are NOT currently tested nor turned on by default:
+
+   - fates_spitfire_mode == 2
+   - fates_spitfire_mode == 5
+   - fates_hydro_solver /= 2DPicard
+   - fates_photosynth_acclimation == kumarathunge2019
+   - fates_cstarvation_model == exponential
+   - fates_stomatal_assimilation = = gross
+   - fates_stomatal_model ==  medlyn2011
+   - fates_leafresp_model ==  atkin2017
+   - use_fates_potentialveg
+   - use_fates_daylength_factor == FALSE
+   - fates_history_dimlevel == 0
+

doc/Quickstart.GUIDE.md

@@ -0,0 +1,68 @@
+# Quick-Start to Using NUOPC Scripts for ctsm6_0
+---
+
+## Assumptions:
+
+You want to use Derecho with ctsm6_0 BGC
+to do a CTSM simulation with data atmosphere and the
+latest CRUJRA atm forcing files and settings. You also want to cycle
+the CRUJRA atm data between 1950 to 2010 and you want to run at
+0.9x1.25 degree resolution.
+
+## Process:
+
+   ### Create the case
+
+``` shell
+   cd cime/scripts
+
+   ./create_newcase --case <testcase> --mach derecho --res f09_t232 -compset I2000Clm60BgcCrop
+   # (./create_newcase -help -- to get help on the script)
+
+   # Setup the case
+
+   cd <testcase>
+   ./xmlchange id1=val1,id2=val2  # to make changes to any settings in the env_*.xml files
+   ./case.setup
+   #(./case.setup -help -- to get help on the script)
+
+   # Add any namelist changes to the user_nl_* files
+
+   $EDITOR user_nl_*
+
+   # Compile the code
+
+   ./case.build
+
+   # Submit the run
+
+   ./case.submit
+
+```
+
+## Information on Compsets:
+
+     "I" compsets are the ones with CTSM and NUOPC driver and CDEPS data models without ice and ocean.
+     Most of the "I" compsets are for clm6_0 physics and use the CRUJRA-2024 data with solar following
+     the cosine of solar zenith angle, precipitation constant, and other
+     variables linearly interpolated in time (and with appropriate time-stamps on
+     the date). Previous CMIP6 simulations with clm5_0 physics used GSWP3 atmospheric forcing.
+
+     To get a list of the "I" compsets use the `query_config` utility in `cime/scripts`
+
+``` shell
+    cd cime/scripts
+    ./query_config --compsets clm
+```
+
+## Automatically resubmitting jobs:
+
+   After doing a short simulation that you believe is correct
+
+``` shell
+   ./xmlchange CONTINUE_RUN=TRUE
+
+   # Change RESUBMIT to number greater than 0, and CONTINUE_RUN to TRUE...
+
+   ./case.submit
+```