run_neon not working as expected

[wwieder]

Brief summary of bug

A few features of the NEON workflow still don't seem to be working as intended, these include

1. Pointing to the wrong ndep and aerosols files
2. Duplications in user_nl_* files that seem to come from cloning a base case and then copying additional information into the user_nl_* files.

The former is potentially a larger issues, while the later is just confusing (at least for me).

General bug information

Examples of both can be found in ad cases here:

/glade/scratch/wwieder/run_NEON_v2/tools/site_and_regional

Specifically BART.ad/user_nl_clm is pointing to

stream_fldfilename_ndep = '$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc'

with BART.ad/user_nl_datm_streams specifying

presaero.SSP3-7.0:datafiles = $DIN_LOC_ROOT/atm/cam/chem/trop_mozart_aero/aero/aerodep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.001_2018-2030_monthly_0.9x1.25_c210826.nc
presaero.SSP3-7.0:year_first=2018

but BART.ad/CaseDocs/datm.streams.xml shows

<stream_info name="presndep.clim_2000">
   <datafiles>      <file>/glade/p/cesmdata/cseg/inputdata/lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc</file>
   </datafiles>

Important details of your setup / configuration so we can reproduce the bug

This code is using ctsm5.1.dev110, with changes to cdeps to try and work around #1858

[wwieder]

@billsacks hopefully this is a simple fix we can bring in with the cdeps tag (once both are ready)?

[wwieder]

I think this is a simple change to cime_config/usermods_dirs/NEON/defaults/shell_commands

./xmlchange DATM_PRESNDEP=SSP3-7.0
./xmlchange DATM_PRESO3=SSP3-7.0

[wwieder]

as well as these additions to cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams

presndep.SSP3-7.0:datafiles = $DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc
presndep.SSP3-7.0:year_first=2018
presndep.SSP3-7.0:year_last=2030
presndep.SSP3-7.0:year_align=2018
presndep.SSP3-7.0:dtlimit=30

preso3.SSP3-7.0:year_first=2018
preso3.SSP3-7.0:year_last=2030
preso3.SSP3-7.0:year_align=2018
preso3.SSP3-7.0:dtlimit=30

[wwieder]

finally, for clarity should we remove the following from cime_config/usermods_dirs/NEON/defaults/user_nl_clm?

stream_fldfilename_ndep = '$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc'