Complete the FATES-CLM nitrogen coupling by slevis-lmwg · Pull Request #3409 · ESCOMP/CTSM

slevis-lmwg · 2025-08-11T21:43:10Z

Description of changes

For now see the issue #3378

Corresponding mods on the FATES side:
NGEET/fates#1472

Nutrient enabled FATES handbook
FATES CLM N coupling

Specific notes

Contributors other than yourself, if any:
@rgknox @adrifoster @wwieder

CTSM Issues Fixed (include github issue #):
#3378

Are answers expected to change (and if so in what way)?
For non-fates tests expect roundoff diffs due to a change in the order of operations in CNNDynamicsMod.F90 as documented below.

Any User Interface Changes (namelist or namelist defaults changes)?
Yes, see changes to CLMBuildNamelist and namelistdefaults.

Does this create a need to change or add documentation? Did you do so?
Yes, no.

Todo: add a modification to the PRT2 test, make sure that prescribed P uptake is set to 10. This will ensure that there are no P limitations in fates, when FATES becomes coupled to CLM's N cycle (in future PR). i:e: fates_cnp_prescribed_puptake=10

Initial testing performed
...with the first two commits in this PR:

PASS ERS_D_Ld30.1x1_brazil.I2000Clm60FatesCrujraRs.derecho_intel.clm-FatesColdPRT2
PASS ERS_D_Ld30.1x1_brazil.I2000Clm60FatesCrujraRs.derecho_intel.clm-FatesCold

Later comments point out that these two tests were inadequate at catching problems, and that I switched to two other tests.

PASS ERS_D_Ld30.1x1_brazil.I2000Clm60FatesCrujraRs.derecho_intel.clm-FatesColdPRT2 FAIL ERS_D_Ld30.1x1_brazil.I2000Clm60FatesCrujraRs.derecho_intel.clm-FatesColdPRT2--clm-mimicsFatesCold--clm-nofireemis The latter needs "nofireemis" to work with Fates, but it then dumps core in line 1180 SoilBiogeochemDecompCascadeMIMICSMod.F90

...calculating these variables: nf_soil%decomp_npools_sourcesink_col nf_soil%fates_litter_flux

slevis-lmwg · 2025-08-13T23:40:21Z

With the latest commit, I repeated the two earlier tests and added another to check whether answers have changed from the baseline:

PASS ERS_D_Ld30.1x1_brazil.I2000Clm60FatesCrujraRs.derecho_intel.clm-FatesColdPRT2
PASS ERS_D_Ld30.1x1_brazil.I2000Clm60FatesCrujraRs.derecho_intel.clm-FatesCold
FAIL ERP_Ld9.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdAllVars -c /glade/campaign/cgd/tss/ctsm_baselines/ctsm5.3.065

The latter fails in case2, after reading the restart file, with a N balance error.

UPDATE

See below for suggestions to resolve FAIL
Add new test ERP_Ld9.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdPRT2 (sanity check first that it meets requirements set forth in the fourth checkbox here, which I think means pointing to an alternate fates paramfile)
Later comment explains why I decided to revert to preexisting ERS tests and skip adding this ERP test.

slevis-lmwg · 2025-08-26T20:48:21Z

Enabled fixation and ran the same tests:

PASS ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdPRT2 -c /glade/campaign/cgd/tss/ctsm_baselines/fates-sci.1.84.0_api.40.0.0-ctsm5.3.066
PASS ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdLUH2 -c /glade/campaign/cgd/tss/ctsm_baselines/fates-sci.1.84.0_api.40.0.0-ctsm5.3.066

PRT2 still b4b with the baseline.
LUH2 now DIFF from the baseline.

PASS The same tests with the code change for harvest (same results relative to the baseline).

...for fates_parteh_mode == 2

slevis-lmwg · 2025-09-20T00:55:38Z

Worked on the next checkbox in the issue (#3378), submitted the same tests, and after some troubleshooting:
PASS PRT2 and b4b with the baseline.
PASS LUH2 and DIFF from the baseline as before.

These variables originate in fates, so this renaming requires the same renaming in fates; I will open the corresponding PR very soon

slevis-lmwg · 2025-09-23T00:04:50Z

OK ./build-namelist_test.pl
OK ./run_sys_tests -s fates -c fates-sci.1.84.0_api.40.0.0-ctsm5.3.066/ --skip-generate
REDO ./run_sys_tests -s aux_clm -c ctsm5.3.066 --skip-generate

Notes:

Gnu and nvhpc tests needed a bug-fix that intel didn't catch (next commit).
Then the fates test-suite worked (I didn't repeat aux_clm for now)
Many tests DIFFer from the baseline.
The PRT2 test had the expected NLCOMP change, though no DIFFs from the baseline (even after rebuilding/rerunning):

  BASE: suplnitro = 'ALL'
  COMP: suplnitro = 'NONE'

slevis-lmwg · 2025-09-23T20:21:06Z

Updated the fates paramfile (see next commit) and submitted these two again

./create_test ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdLUH2 -c /glade/campaign/cgd/tss/ctsm_baselines/fates-sci.1.84.0_api.40.0.0-ctsm5.3.066
./create_test ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdPRT2 -c /glade/campaign/cgd/tss/ctsm_baselines/fates-sci.1.84.0_api.40.0.0-ctsm5.3.066

The first (LUH2) same as before (DIFF from baseline) since nothing changed for it.
The second (ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdPRT2.C.20250923_141838_qjxqou) now:

DIFF from baseline and
FAIL COMPARE_base_rest suggesting variable(s) missing from restart, I suspect

Simplify messaging during docs build slevis resolved conflicts: bld/namelist_files/namelist_defaults_ctsm.xml

slevis-lmwg · 2026-04-13T19:13:20Z

Testing on derecho after the latest updates:

./run_sys_tests -s fates -c fates-sci.1.92.0_api.44.0.0-ctsm5.4.031 --skip-generate
build-namelist_test.pl

Before I try ./run_sys_tests -s aux_clm -c ctsm5.4.032 --skip-generate, I will look into the diffs from baseline with this test from the above list of failures:
SMS_Ld5.f10_f10_mg37.I1850Clm45BgcCrop.derecho_intel.clm-crop
Largest diffs (grepped for "E-0") out of a total of 53 fields with non-zero diffs suggest roundoff diffs:

 RMS CH4_SURF_AERE_SAT                2.0582E-10            NORMALIZED  3.9956E-03
 RMS CH4_SURF_DIFF_SAT                8.6639E-14            NORMALIZED  1.6418E-04
 RMS FCH4                             4.7957E-15            NORMALIZED  1.3812E-04
 RMS FCH4TOCO2                        4.7907E-12            NORMALIZED  8.6788E-05
 RMS FCH4_DFSAT                       8.9717E-20            NORMALIZED  2.3733E-07
 RMS NEM                              4.7907E-12            NORMALIZED  1.2779E-04
 RMS SOM_C_LEACHED                    1.3173E-25            NORMALIZED  1.5688E-09
 RMS TOTCOLCH4                        6.1704E-10            NORMALIZED  1.9915E-09
 RMS CONC_O2_SAT                      4.7118E-03            NORMALIZED  4.4369E-02

The test gives similar/same diffs when I reverse the mods in SoilBiogeochemCompetitionMod.F90
The test returns b4b when I reverse the mods in CNNDynamicsMod.F90
Starting aux_clm to confirm all DIFFs go away, though Fates tests appear to fail now

slevis-lmwg · 2026-04-14T18:19:45Z

Now repeat ./run_sys_tests -s aux_clm -c ctsm5.4.032 --skip-generate with the latest commit:

izumi
derecho
Three tests ran out of walltime that didn't fail before, so I will not spend additional time on them for now:

ERS_Ly5_Mmpi-serial.1x1_smallvilleIA.I1850Clm50BgcCrop.derecho_gnu.clm-ciso_monthly RUN
ERS_Ly5_Mmpi-serial.1x1_smallvilleIA.I1850Clm50BgcCrop.derecho_gnu.clm-ciso_monthly--clm-matrixcnOn RUN
ERS_Ly5_P128x1.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-cropMonthOutput--clm-matrixcnOn_ignore_warnings RUN

Known issue #3840

slevis-lmwg · 2026-04-14T22:16:10Z

@rgknox testing seems satisfactory to me, so this PR and its fates counterpart are ready for your final review, unless you think of anything else that we need to work on here.

glemieux

This looks good. Thanks again to @slevis-lmwg for the walkthrough. I just have two questions/comments that should be dealt with via other PRs (if at all).

glemieux · 2026-04-17T22:37:55Z

 'FATES_DEMOTION_CARBONFLUX', 'FATES_PROMOTION_CARBONFLUX',
 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_USTORY',
 'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL',
-'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC',


Do we have an issue to note why this shouldn't be included here? I could find anything specific outside of a conflict with using it during ST3 or SP mode tests.

glemieux · 2026-04-17T22:49:09Z

+  <test name="ERS_D_Ld30" grid="f45_f45_mg37" compset="I2000Clm60FatesRs" testmods="clm/FatesColdPRT2_suplnAll">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>


@rgknox do you use lawrencium? We should instances of lawrencium if we don't think we're going to be using it anytime soon, but that's out of scope for this PR so I'd just make an issue if you agree.

slevis-lmwg added 2 commits July 30, 2025 15:30

Uncomment if ( .not. use_fates_sp ) section of clmfates_interfaceMod

01671b9

...calculating these variables: nf_soil%decomp_npools_sourcesink_col nf_soil%fates_litter_flux

slevis-lmwg self-assigned this Aug 11, 2025

slevis-lmwg linked an issue Aug 11, 2025 that may be closed by this pull request

Completing the FATES-CLM nitrogen coupling #3378

Open

1 task

slevis-lmwg added 4 commits August 12, 2025 16:45

Replace plant_ndemand(c) * nuptake_prof(c,j) with plant_ndemand_vr(c,j)

59f9d09

New use_fates section for plant_ndemand_vr and plant_ndemand from fates

b155e58

New use_fates section to set the FATES N uptake fluxes

c79230c

Change clm_fate from "in" to "inout" argument

98b4b7d

slevis-lmwg commented Aug 14, 2025

View reviewed changes

Comment thread src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90 Outdated

slevis-lmwg commented Aug 14, 2025

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Comment thread src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90

slevis-lmwg added 4 commits August 14, 2025 17:27

Replace if (use_fates) with (is_fates(c)) to add flexibility

a46a76c

Remove two unhelpful 1x1 FatesColdPRT2 tests that I added earlier

f2202fb

New is_fates section for plant_ndemand, now when use_nitrif_denitrif

e96b87e

Add (really, uncomment) FATES npp to enable fixation

b24738b

slevis-lmwg added 2 commits September 19, 2025 17:24

Uncomment hrv_deadstem_to_prod* lines in clmfates_interfaceMod

00a332e

...for fates_parteh_mode == 2

Add error check about fates_parteh_mode = 2 and suplnitro = suplnAll

2bbdd64

slevis-lmwg added 2 commits September 22, 2025 16:52

Upd. namelist_defaults for suplnitro when parteh_mode == 1 or /= 1

d8bc6ce

prt_carbon_allom_hyp -> fates_c_only & prt_cnp_flex_allom_hyp ->fates_cn

116b310

These variables originate in fates, so this renaming requires the same renaming in fates; I will open the corresponding PR very soon

slevis-lmwg mentioned this pull request Sep 22, 2025

Complete the FATES-CLM nitrogen coupling NGEET/fates#1472

Open

5 tasks

Correction to syntax error caught by gnu and nvhpc, not intel

ba955b6

slevis-lmwg added 5 commits April 13, 2026 11:34

Simplify elsif in CLMBuildNamelist.pm to get past failure

911f307

Correct minor typo

d7d8a22

Add 2 expected failure tests to build-namelist_test.pl

f798627

Merge tag 'ctsm5.4.032' into fates-cn

488b93c

Simplify messaging during docs build slevis resolved conflicts: bld/namelist_files/namelist_defaults_ctsm.xml

Update to existing compsets in new PRT2 tests for cases to create

83bf1f1

slevis-lmwg commented Apr 13, 2026

View reviewed changes

Comment thread src/biogeochem/CNNDynamicsMod.F90

slevis-lmwg commented Apr 13, 2026

View reviewed changes

Comment thread src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90

slevis-lmwg commented Apr 13, 2026

View reviewed changes

Comment thread src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90

slevis-lmwg added this to LMWG: Sprint Planning Board Apr 14, 2026

github-project-automation bot moved this to Todo in LMWG: Sprint Planning Board Apr 14, 2026

slevis-lmwg moved this from Todo to In Progress in LMWG: Sprint Planning Board Apr 14, 2026

slevis-lmwg moved this from In Progress to Todo in LMWG: Sprint Planning Board Apr 14, 2026

slevis-lmwg moved this from Todo to Stalled in LMWG: Sprint Planning Board Apr 14, 2026

slevis-lmwg mentioned this pull request Apr 15, 2026

Tests that needed longer wallclock #3840

Open

wwieder modified the milestone: FATES freeze for ctsm6 Apr 16, 2026

wwieder requested review from glemieux April 16, 2026 16:59

slevis-lmwg removed the request for review from rgknox April 16, 2026 20:35

slevis-lmwg added this to CTSM: Upcoming tags Apr 20, 2026

github-project-automation bot moved this to Ready to start (or start again) in CTSM: Upcoming tags Apr 20, 2026

slevis-lmwg moved this from Ready to start (or start again) to In progress - master in CTSM: Upcoming tags Apr 20, 2026

slevis-lmwg moved this from Stalled to In Progress in LMWG: Sprint Planning Board Apr 20, 2026

glemieux approved these changes Apr 20, 2026

View reviewed changes

glemieux added this to FATES Pull Request Planning and Status Apr 20, 2026

glemieux moved this to Under Review in FATES Pull Request Planning and Status Apr 20, 2026

glemieux requested a review from samsrabin April 20, 2026 19:33

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