PPE parameter work -Addresses issues 2830 and 2831

[olyson]

Description of changes

b4b moves of namelist variables to parameter file for PPE per issue #2830 and make some parameter variables pft-dimensioned per #2831

Note that baseflow_scalar and pot_hmn_ign_counts_alpha were not moved from namelist to parameter file due to reasons detailed in #2830

Specific notes

Contributors other than yourself, if any: @slevis-lmwg helped troubleshoot testing issues

CTSM Issues Fixed (include github issue #): #2830 , #2831

Are answers expected to change (and if so in what way)? No

Any User Interface Changes (namelist or namelist defaults changes)? Yes

Does this create a need to change or add documentation? Did you do so? No

Testing performed, if any:
Compare to ctsm5.3.009
Derecho aux_clm: PASS except for (not sure why the baseline files are missing, the last one is ok since it is a new test):

    FAIL ERP_D_P64x2_Ld3.f10_f10_mg37.I2000Clm50BgcCru.derecho_gnu.clm-default BASELINE ctsm5.3.009: ERROR BFAIL some baseline files were missing
    FAIL ERP_Ld5.f10_f10_mg37.I1850Clm50Bgc.derecho_gnu.clm-default BASELINE ctsm5.3.009: ERROR BFAIL some baseline files were missing
    FAIL ERS_D_Ld3.f10_f10_mg37.I1850Clm50BgcCrop.derecho_gnu.clm-default BASELINE ctsm5.3.009: ERROR BFAIL some baseline files were missing
    FAIL ERS_D_Ld6.f10_f10_mg37.I1850Clm45BgcCrop.derecho_gnu.clm-clm50CMIP6frc BASELINE ctsm5.3.009: ERROR BFAIL some baseline files were missing
    FAIL ERS_Ld3_D.f10_f10_mg37.I1850Clm50BgcCrop.derecho_gnu.clm-rad_hrly_light_res_half BASELINE ctsm5.3.009: ERROR BFAIL some baseline files were missing
    FAIL SMS_D.f10_f10_mg37.I2000Clm60Bgc.derecho_gnu BASELINE ctsm5.3.009: ERROR BFAIL some baseline files were missing
    FAIL SMS_Ln9.ne3pg3_ne3pg3_mg37.I2000Clm50Sp.derecho_gnu.clm-clm50cam6LndTuningMode--clm-nofireemis BASELINE ctsm5.3.009: ERROR BFAIL some baseline files were missing
    FAIL ERI_Ld9.f45_g37.I2000Clm50BgcCru.derecho_intel.clm-nofire BASELINE ctsm5.3.009: ERROR BFAIL some baseline files were missing
    FAIL ERS_D_Ld9.ne30pg3_t232.I1850Clm60BgcCropG.derecho_intel.clm-clm60cam7LndTuningMode BASELINE ctsm5.3.009: ERROR BFAIL some baseline files were missing
    FAIL SMS_Lm1.f10_f10_mg37.I1850Clm60Bgc.derecho_intel.clm-clm60_monthly_matrixcn_soilCN30 BASELINE ctsm5.3.009: ERROR BFAIL baseline directory '/glade/campaign/cgd/tss/ctsm_baselines/ctsm5.3.009/SMS_Lm1.f10_f10_mg37.I1850Clm60Bgc.derecho_intel.clm-clm60_monthly_matrixcn_soilCN30' does not exist

Izumi aux_clm: PASS except for (ok though):

PEND SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-NEON-MOAB--clm-PRISM SHAREDLIB_BUILD (UNEXPECTED: expected FAIL)

nohup ./build-namelist_test.pl PASS
./run_ctsm_py_tests -u PASS (OK)
./run_ctsm_py_tests -s PASS (OK)

[slevis-lmwg]

@olyson thank you for your work in this PR. My comments are mostly minor. The one about whether to read params in pftconMod or locally is a bit bigger, and I'm not certain whether it's relevant and worth considering.

[olyson]

I think this is ready for re-review. Thanks for the input @slevis-lmwg .
I've moved the read of jmaxb0, jmaxb1, wc2wjb0 from pftconMod to LunaMod and r_mort to CNGapMortality.
Also, made adjustment to r_mort for use_cndv.
Testing results are exactly the same as reported previously.
I have not changed the paths to the parameter files yet in case there are more changes and testing.

[olyson]

I see now that @slevis-lmwg has rimported the parameter files so I have changed the paths accordingly.
A question I have is that I see this when I ran build-namelist_text.pl:

Looks like you planned 3997 tests but ran 3996.

Does this have anything to do with the jmax test I removed? Is there something else I should remove?

[olyson]

@slevis-lmwg , it looks like permissions need to be changed on those parameter files, thanks.

[slevis-lmwg]

I see now that @slevis-lmwg has rimported the parameter files so I have changed the paths accordingly. A question I have is that I see this when I ran build-namelist_text.pl:

Looks like you planned 3997 tests but ran 3996.

Does this have anything to do with the jmax test I removed? Is there something else I should remove?

Yes, this is due to the removed test. My experience tells me that the number of planned tests affects nothing more than the message to the screen. You are welcome to update the number of planned tests, which is hardwired in the build-namelist_test.pl script (just search for 3997 in this case). I usually do so when I see a discrepancy between "planned" and "ran" numbers.

[slevis-lmwg]

@slevis-lmwg , it looks like permissions need to be changed on those parameter files, thanks.

Done and thank you for the reminder!