Make certain history fields descriptive that have been labeled by number since #1340 #1413

slevis-lmwg · 2021-06-26T21:28:03Z

Description of changes

I use existing infrastructure to add descriptive strings to certain history fields that I had labeled by number in #1340

Specific notes

Contributors other than yourself, if any:
@wwieder @ekluzek

CTSM Issues Fixed (include github issue #):
Fixes #1392

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

Any User Interface Changes (namelist or namelist defaults changes)?
No

Testing performed, if any:
./create_test ERP_D_Ld3_P36x2.f10_f10_mg37.I2000Clm50BgcCru.cheyenne_intel.clm-default -c /glade/p/cgd/tss/ctsm_baselines/ctsm5.1.dev043
where I made the C12 and the N variables active temporarily.
The test passed with the only diff. from baseline as follows:

Could not find match for file1 variable DWT_FROOTC_TO_LITR_CEL_C in file2
Could not find match for file1 variable DWT_FROOTC_TO_LITR_LIG_C in file2
Could not find match for file1 variable DWT_FROOTC_TO_LITR_MET_C in file2
Could not find match for file1 variable DWT_FROOTN_TO_LITR_CEL_N in file2
Could not find match for file1 variable DWT_FROOTN_TO_LITR_LIG_N in file2
Could not find match for file1 variable DWT_FROOTN_TO_LITR_MET_N in file2

as expected. Previously these fields would have been numbered instead of labeled CEL, LIG, MET.

slevis-lmwg · 2021-06-26T21:36:55Z

I started a new branch for this PR continuing from the branch in PR #1400 so that I could make progress while #1400 wasn't merged. So really the first commit in this PR is f179d0a

slevis-lmwg · 2021-06-26T22:00:17Z

My work this far in this PR has resolved the problem that I introduced in #1340 for certain litter fields.

Next I will update the handling of other history fields that still get labeled by number instead of by descriptive string.

slevis-lmwg · 2021-06-26T23:31:20Z

src/biogeochem/CNVegCarbonFluxType.F90

-          fieldname = 'DWT_FROOTC_TO_LITR_'//trim(decomp_cascade_con%decomp_pool_name_short(k))//'_C'
-          longname =  'fine root to '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' litter due to landcover change'
+          fieldname = 'DWT_FROOTC_TO_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_C'
+          longname =  'fine root to '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' due to landcover change'


Here and elsewhere I have now removed the hardwired strings "LITR_" and "litter" and placed them in decomp_pool_name_history and decomp_pool_name_long.

slevis-lmwg · 2021-06-26T23:37:37Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

-      decomp_cascade_con%decomp_pool_name_short(i_met_lit) = 'MET'
+      decomp_cascade_con%decomp_pool_name_history(i_met_lit) = 'MET_LIT'
+      decomp_cascade_con%decomp_pool_name_long(i_met_lit) = 'metabolic litter'
+      decomp_cascade_con%decomp_pool_name_short(i_met_lit) = 'L1'


Here and elsewhere I updated decomp_pool_name_history and decomp_pool_name_long with descriptive names rather than numbers. However:

I kept decomp_pool_name_restart unchanged because otherwise I lost the bfb answers with baseline.

I returned decomp_pool_name_short to the original non-descriptive names to maintain the option of truly short names. These came in handy for certain history fields that otherwise triggered an error by exceeding some length.

This also means having to update the master history list that shows up in the documentation:
doc/source/users_guide/setting-up-and-running-a-case/master_list_file.rst
I will wait to confirm that this is what you want me to do @wwieder @ekluzek

I realized this because 6 cheyenne tests failed with the error
LITR1C_TO_SOIL1C in fincl( 22 ) for history tape 1 not found

Otherwise both test-suites were OK.

Yes, this sounds.

slevis-lmwg · 2021-06-26T23:47:59Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

-      decomp_cascade_con%decomp_pool_name_history(i_pro_som) = 'SOIL1'
-      decomp_cascade_con%decomp_pool_name_long(i_pro_som) = 'soil 1'
+      decomp_cascade_con%decomp_pool_name_history(i_pro_som) = 'PAS_SOM'
+      decomp_cascade_con%decomp_pool_name_long(i_pro_som) = 'passive soil organic matter'


@wwieder let's make sure that I labeled the three SOMs correctly. In the first refactor I had chosen other names for the corresponding indices:

i_pro_som for "protected"

i_rec_som for "recalcitrant"

i_avl_som for "available"

If I have now correctly mapped "protected" to "passive", "recalcitrant" to "slow", and "available" to "active", then I think I should also rename the indices for consistency to i_pas_som, i_slo_som, and i_act_som. Let me know if you disagree.

This is likely fine, but we should add carbon and nitrogen to both name_history and name_long (as is done with the BGC / CENTURY pools).

To your other question, let's go ahead and call the pools active, slow and passive (this is more consistent with the CENTURY language). And, yes, your mapping is correct.

This is likely fine, but we should add carbon and nitrogen to both name_history and name_long (as is done with the BGC / CENTURY pools).

The C/carbon and N/nitrogen labels get added to the history fields when the variables are written to history. This way the section of the code that we are looking at here can exist once for both C and N.

slevis-lmwg · 2021-06-26T23:52:33Z

src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90

@@ -340,7 +340,7 @@ subroutine InitHistory(this, bounds)
          data1dptr => this%decomp_cascade_sminn_flux_col(:,l)
          if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then
             fieldname = 'SMINN_TO_'//&
-                  trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))//'N_'//&
+                  trim(decomp_cascade_con%decomp_pool_name_short(decomp_cascade_con%cascade_receiver_pool(l)))//'N_'//&


Here and in one other place I replaced decomp_pool_name_history with decomp_pool_name_short because I got an error as a result of a fieldname that was too long.

The longname still contains all the necessary information for users to decipher which variable they are looking at.

Yes, this makes sense.

slevis-lmwg · 2021-06-28T21:39:01Z

cime_config/usermods_dirs/output_bgc/user_nl_clm

-hist_fexcl1 += 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'SOILC_vr','SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr', 'CWDN_vr', 'SMIN_NO3_vr', 'CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr'
-hist_fincl1 += 'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','LITR1C_TO_SOIL1C','LITR1N_TO_SOIL1N','LITR2C_TO_SOIL1C', 'LITR2N_TO_SOIL1N','LITR3C_TO_SOIL2C','LITR3N_TO_SOIL2N','DWT_WOOD_PRODUCTC_GAIN_PATCH'
+hist_fexcl1 += 'PAS_SOMC_vr', 'PAS_SOMN_vr', 'SLO_SOMC_vr', 'SLO_SOMN_vr', 'ACT_SOMC_vr', 'ACT_SOMN_vr', 'SOILC_vr','SOILN_vr', 'CWDC_vr', 'MET_LITC_vr', 'CEL_LITC_vr', 'LIG_LITC_vr', 'MET_LITN_vr', 'CEL_LITN_vr', 'LIG_LITN_vr', 'CWDN_vr', 'SMIN_NO3_vr', 'CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr'
+hist_fincl1 += 'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','MET_LITC_TO_PAS_SOMC','MET_LITN_TO_PAS_SOMN','CEL_LITC_TO_PAS_SOMC', 'CEL_LITN_TO_PAS_SOMN','LIG_LITC_TO_SLO_SOMC','LIG_LITN_TO_SLO_SOMN','DWT_WOOD_PRODUCTC_GAIN_PATCH'


Cheyenne test-suite now OK (with the changes to this file).

Izumi test-suite was already OK before.

Now only doc/source/users_guide/setting-up-and-running-a-case/master_list_file.rst (i.e. the documentation) is inconsistent.

as with other files, SOIL1C needs to be ACT_SOM

New stream functionality when using NUOPC or LILAC This tag creates new stream functionality when using the NUOPC and LILAC caps, and maintains backwards compatibility with the older CPL7 stream functionality when using the MCT cap. - New stream code has been placed in src/cpl/share_esmf (so that they can also be leveraged by LILAC) - Older stream code for mct is now in src/cpl/mct - LILAC interface has been changed to leverage the new stream code as well Where possible share code was used. In particular, this holds for SatellitePhenologyMod.F90. Resolved Conflicts: doc/ChangeLog doc/ChangeSum

Params file sets the respiration fractions for CWD to zero: rf_cwdl2_bgc = 0 rf_cwdl3_bgc = 0 The model has no code to handle rf_cwd* > 0. So... - I have introduced cwdhr_col to track this HR the same way that we track lithr_col for litter. - I have removed if-statements that prevented CWD HR pools and decomposition from writing to history. - I have introduced a new test to the cheyenne test-suite that makes active seven history fields pertaining to CWD HR and points to a params file with rf_cwd* > 0. I have confirmed that the new test returns the new active variables as greater than 0 when pointing to the new params file and equal to 0 when pointing to the default params file. NB: This branch and PR ESCOMP#1413 started from ESCOMP#1400 which already included almost all the code that would have otherwise come in with this merge. Resolved Conflicts: doc/ChangeLog doc/ChangeSum

slevis-lmwg · 2021-06-30T19:27:09Z

I have now rebuilt the official documentation. I will wait for this PR to be merged before pushing the new documentation.

slevis-lmwg · 2021-06-30T19:34:47Z

Now that I updated to dev045,
"Changes from all commits" shows ONLY the changes that I made in this PR.

wwieder · 2021-07-01T16:01:18Z

@slevisconsulting what's the status on this?

slevis-lmwg · 2021-07-01T16:19:01Z

Ready for final review and line-up for merge. As soon as I hear that this PR is next in line, I can rerun the test-suites.

wwieder · 2021-07-01T16:24:47Z

@ekluzek can you coordinate with @slevisconsulting on timing for this PR?

wwieder

Throughout S1 should correspond to active SOM, and S3 should be passive. Sorry for the confusion @slevisconsulting

wwieder · 2021-07-01T16:29:56Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

-      is_metabolic(i_avl_som) = .false.
-      is_cellulose(i_avl_som) = .false.
-      is_lignin(i_avl_som) = .false.
+      i_pas_som = i_lig_lit + 1


This should be active SOM (S1)? Passive should be the last pool (S3).

Thank you for catching @wwieder! I will correct this later today.

wwieder · 2021-07-01T16:31:22Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

+      is_cellulose(i_slo_som) = .false.
+      is_lignin(i_slo_som) = .false.
+
+      i_act_som = i_slo_som + 1


and here these fields should be the passive SOM(S3), NOT active

wwieder · 2021-07-01T16:31:57Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

@@ -480,10 +480,10 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i
         spinup_factor(i_cwd) = max(1._r8, (speedup_fac * params_inst%tau_cwd_bgc / 2._r8 ))
      end if
      !som1
-      spinup_factor(i_pro_som) = 1._r8
+      spinup_factor(i_pas_som) = 1._r8


again, this should be active, slow passive for S1, S2, S3, respectively

wwieder · 2021-07-01T16:32:19Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

@@ -495,56 +495,56 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i
      decomp_cascade_con%cascade_step_name(i_l1s1) = 'L1S1'
      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l1s1) = rf_l1s1
      cascade_donor_pool(i_l1s1) = i_met_lit
-      cascade_receiver_pool(i_l1s1) = i_pro_som
+      cascade_receiver_pool(i_l1s1) = i_pas_som


again, active here and the in lines below

wwieder · 2021-07-01T16:33:21Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l3s2) = 1.0_r8

      i_s1s2 = 4
      decomp_cascade_con%cascade_step_name(i_s1s2) = 'S1S2'
      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s1s2) = rf_s1s2(bounds%begc:bounds%endc,1:nlevdecomp)
-      cascade_donor_pool(i_s1s2) = i_pro_som
-      cascade_receiver_pool(i_s1s2) = i_rec_som
+      cascade_donor_pool(i_s1s2) = i_pas_som


again S1 should be active

wwieder · 2021-07-01T16:33:42Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

-      cascade_donor_pool(i_s2s3) = i_rec_som
-      cascade_receiver_pool(i_s2s3) = i_avl_som
+      cascade_donor_pool(i_s2s3) = i_slo_som
+      cascade_receiver_pool(i_s2s3) = i_act_som


and passive here for S3

wwieder · 2021-07-01T16:34:13Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

      pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s2s3) = f_s2s3

      i_s3s1 = 8
      decomp_cascade_con%cascade_step_name(i_s3s1) = 'S3S1'
      rf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s3s1) = rf_s3s1
-      cascade_donor_pool(i_s3s1) = i_avl_som
-      cascade_receiver_pool(i_s3s1) = i_pro_som
+      cascade_donor_pool(i_s3s1) = i_act_som


switch here

wwieder · 2021-07-01T16:36:21Z

src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90

               depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_s2(c)
-            decomp_k(c,j,i_avl_som) = k_s3    * t_scalar(c,j) * w_scalar(c,j) * &
+            decomp_k(c,j,i_act_som) = k_s3    * t_scalar(c,j) * w_scalar(c,j) * &


again, switch active and passive here (S1 and S3, respectively)

wwieder · 2021-07-01T16:40:10Z

cime_config/usermods_dirs/output_bgc/user_nl_clm

-hist_fexcl1 += 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'SOILC_vr','SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr', 'CWDN_vr', 'SMIN_NO3_vr', 'CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr'
-hist_fincl1 += 'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','LITR1C_TO_SOIL1C','LITR1N_TO_SOIL1N','LITR2C_TO_SOIL1C', 'LITR2N_TO_SOIL1N','LITR3C_TO_SOIL2C','LITR3N_TO_SOIL2N','DWT_WOOD_PRODUCTC_GAIN_PATCH'
+hist_fexcl1 += 'PAS_SOMC_vr', 'PAS_SOMN_vr', 'SLO_SOMC_vr', 'SLO_SOMN_vr', 'ACT_SOMC_vr', 'ACT_SOMN_vr', 'SOILC_vr','SOILN_vr', 'CWDC_vr', 'MET_LITC_vr', 'CEL_LITC_vr', 'LIG_LITC_vr', 'MET_LITN_vr', 'CEL_LITN_vr', 'LIG_LITN_vr', 'CWDN_vr', 'SMIN_NO3_vr', 'CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr'
+hist_fincl1 += 'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','MET_LITC_TO_PAS_SOMC','MET_LITN_TO_PAS_SOMN','CEL_LITC_TO_PAS_SOMC', 'CEL_LITN_TO_PAS_SOMN','LIG_LITC_TO_SLO_SOMC','LIG_LITN_TO_SLO_SOMN','DWT_WOOD_PRODUCTC_GAIN_PATCH'


as with other files, SOIL1C needs to be ACT_SOM

I had assigned passive SOM to soil1 and active SOM to soil3 and should have assigned them the other way around. The correction results in a modified master_list_file.rst. I have rebuilt the official documentation and will push when this PR gets merged.

slevis-lmwg · 2021-07-01T21:24:02Z

Again, thank you for catching this mistake @wwieder !

ekluzek · 2021-07-09T05:51:46Z

@slevisconsulting this should be updated to ctsm5.1.dev047 and run the full testing on it, and then bring it in as ctsm5.1.dev048.

Start bounds at 1; remove references to MCT Users: take note of (1), and in particular the caveat for users noted below (in the "Notes of particular relevance for users"). (1) All global index arrays on a given processor now have a starting index of 1 - bounds_proc for each subgrid level has a starting index of 1 for each level - bounds_clump for each subgrid level has a starting index of 1 for just the first clump on the processor - but all the other clumps on the processor do not start at 1 - but rather are offset with the number of gridcells, columns, ...etc on the preceeding clumps (2) There are no longer any references to any mct data structures other than in the mct cap - All references to gsmap have been removed from decompMod.F90 and replaced with new global index arrays for the various subgrid levels - decompInitMod has been refactored to calculated these global index arrays using pure MPI rather than mct - ncdio_pio_F90.in has been refactored to use the new global index arrays rather than the gsmap data structures - the data struture ldecomp is no longer needed - the module spmdGathScatMod.F90 is no longer needed and has been removed Resolved Conflicts: doc/ChangeLog doc/ChangeSum

slevis-lmwg · 2021-07-09T23:48:10Z

Cheyenne test-suite OK
TPUTCOMP non-passes: 4
MEMCOMP non-passes: 25

Izumi test-suite OK

Make history fields descriptive instead of labeling by number

f179d0a

Make more history fields descriptive instead of labeling by number

304f16c

slevis-lmwg commented Jun 26, 2021

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slevis-lmwg requested review from ekluzek and wwieder June 26, 2021 23:58

slevis-lmwg self-assigned this Jun 26, 2021

slevis-lmwg linked an issue Jun 26, 2021 that may be closed by this pull request

Some soil decomposition history fields have the pool number rather than a description in their name #1392

Closed

slevis-lmwg added the enhancement new capability or improved behavior of existing capability label Jun 27, 2021

slevis-lmwg added 4 commits June 28, 2021 15:03

Rename i_[pro,rec,avl]_som --> i_[pas,slo,act]_som

5c0ef4f

Minor update to comments about soil organic matter (SOM)

3b73e57

Minor comment update

a34d2c5

Update fincl and fexcl lists to new history field names

85bf70f

slevis-lmwg commented Jun 28, 2021

View reviewed changes

slevis-lmwg added 4 commits June 28, 2021 16:15

First draft of updated ChangeLog

34c26e7

Updating master_list_fie.rst (official documentation not rebuilt, yet)

22d4162

Small correction to ChangeLog

0b84f8b

wwieder requested changes Jul 1, 2021

View reviewed changes

slevis-lmwg added 2 commits July 1, 2021 15:03

Additional correction in response to review

5bf6ae3

wwieder approved these changes Jul 2, 2021

View reviewed changes

ekluzek approved these changes Jul 9, 2021

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slevis-lmwg and others added 2 commits July 9, 2021 17:55

Updated ChangeLog

8c3570a

Update change files

5176e76

ekluzek merged commit 05c1eae into ESCOMP:master Jul 10, 2021

ekluzek deleted the 1392_starting_from_1400 branch July 10, 2021 17:41

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Make certain history fields descriptive that have been labeled by number since #1340 #1413

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Make certain history fields descriptive that have been labeled by number since #1340 #1413

Make certain history fields descriptive that have been labeled by number since #1340 #1413

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