Complete the FATES-CLM nitrogen coupling #3409

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)?

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

Does this create a need to change or add documentation? Did you do so?

[ ] 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

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.

src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90

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

slevis-lmwg · 2025-10-18T00:14:32Z

Submitted the same 2 tests

./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

now with the error check suggested in NGEET/fates#1454 (see corresponding commit NGEET/fates@97839f1 in NGEET/fates#1472)

PRT2 same behavior: variable(s) missing from restart?
LUH2 FAIL triggered the new error message (turns out it shouldn't have, yet, becase fates_parteh_mode was 1):

hlm_name cannot be CLM while prescribed_puptake == 0, because the CLM does not do prognostic phosphorus. Exiting.
ERROR in FatesInterfaceMod.F90 at line 919

UPDATE Repeating with 2025/12/10 updates:

PRT2 same behavior: COMPARE_base_rest
LUH2 didn't trigger the new error message in its new location and passed, as expected; when I added fates_parteh_mode = 2, another similar error got triggered, and Ryan and I decided to keep the latter and remove the former
Test on izumi 2025/12/16 while derecho is down (gnu, intel, nag):
ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_*.clm-FatesColdLUH2 FAILs in RUN as per FATES landuse default fluh_timeseries crashes FatesColdLUH test on izumi #2653, so I tried
PASS ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesRs.izumi_nag.clm-FatesCold with parteh_mode = 1
FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesRs.izumi_nag.clm-FatesCold with parteh_mode = 2 as expected
Troubleshoot restart issue (SL, but also Ryan offered to look into it)
- FAIL ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdPRT2 as expected FATES PRT2 test failing on izumi_nag #3183 but it may work if I shorten the test to Ld10
- Return to derecho: UPDATED my fates-cn branches to ctsm5.4.004/sci.1.88.0_api.42.0.0
  LUH2 DIFF from latest baseline fates-sci.1.88.0_api.42.0.0-ctsm5.4.001 EXPECTED due to update to .004
  PRT2 FAIL COMPARE_base_rest
- The first post mentioning the restart problem made me think of rerunning the original PRT2 against the latest baseline fates-sci.1.89.0_api.43.0.0-ctsm5.4.005 without 391a023 and that PASSed despite the NLCOMP change of suplnitro from 'ALL' to 'NONE'.
Add new tests (from meeting with Ryan 2025/12/16):
- PRT2_synthN (nuptake = 10) to reproduce what used to happen before coupling
- PRT2_suplnAll that swaps namelist setting suplnitro to suplnAll. Initially I tested this in the existing PRT2 test, and it exited with an expected namelist error:

ERROR : CLMBuildNamelist::setup_logic_supplemental_nitrogen() : supplemental Nitrogen (suplnitro) is NOT set to NONE, FATES is on, and FATES-SP is not active, but fates_parteh_mode is 2, so Nitrogen is active; change suplnitro back to NONE

slevis-lmwg · 2025-12-17T01:33:03Z

The reason for the last commit is explained in #2653 (comment).

Update crop parameters and maturity requirements slevis resolved conflicts: src/fates <-- So far I have not changed .gitmodules to point to my branch src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90

FATES JSON parameter files These changes accommodate a JSON format to the FATES parameter file. Documentation has been updated in the FATES User's Guide: https://fates-users-guide.readthedocs.io/en/latest/user/Parameter-File.html fates was updated from sci.1.88.0_api.42.0.0 to sci.1.89.0_api.43.0.0 ESCOMP and NGEET PRs: ESCOMP#3570 NGEET/fates#1493 slevis resolved conflicts: cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/shell_commands cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm src/fates

slevis-lmwg · 2025-12-20T00:43:34Z

After the latest updates, I'm submitting these tests with ./create_test:

PASS ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdPRT2_synthN
BASELINE ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdLUH2
COMPARE_base_rest ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdPRT2

LUH2 diffs from fates-sci.1.89.0_api.43.0.0-ctsm5.4.005:
FATES_HET_RESP 7.5810E-16 NORMALIZED 2.1208E-07
FATES_NEP 7.5810E-16 NORMALIZED 2.8903E-07

PRT2 diffs in the same 38 fields in base.cprnc.out as in cprnc.out.

Ryan thinks that the restart problem comes from the FATES side because the problem appears when nitrogen becomes interactive
For troubleshooting, it may help to run 2 time steps in single-point, possibly turning off pieces of code, e.g. any litter generation and exudation
@rgknox offered to start some of this troubleshooting

slevis-lmwg · 2025-12-26T17:08:02Z

bld/CLMBuildNamelist.pm

+    if ( ($parteh_mode == 2) &&  ($suplnitro !~ /NONE/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
+      $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to NONE, FATES is on, " .
+                        "and FATES-SP is not active, but fates_parteh_mode is 2, so Nitrogen is active; " .
+                        "change suplnitro back to NONE");


Remove this new check because in parteh_mode = 2 we want to allow either NONE or ALL suplnitro.

Or replace check with not allowing parteh_mode = 2 and sp mode together.

slevis-lmwg · 2025-12-26T17:08:40Z

bld/CLMBuildNamelist.pm

+
+    my $parteh_mode = $nl->get_value('fates_parteh_mode');
+    if ( ($parteh_mode == 1) &&  ($suplnitro !~ /ALL/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
+      $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " .
+                        "and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active. " .
+                        "Change suplnitro back to ALL");


Here remove the sp condition because irrelevant.

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

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slevis-lmwg commented Aug 14, 2025

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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

Update fates paramfile var prescribed_puptake to 1 for PRT2 test

391a023

slevis-lmwg added 2 commits December 8, 2025 12:28

Adjust unit conversions to agree with FATES commit b2a1da6

e881a89

Change fates paramfile var prescribed_puptake to 10 for PRT2 test

8135820

slevis-lmwg mentioned this pull request Dec 11, 2025

Completing the FATES-CLM nitrogen coupling #3378

Open

1 task

Replace fates_cn with fates_cnp throughout

e73b42d

slevis-lmwg marked this pull request as ready for review December 16, 2025 19:26

slevis-lmwg requested a review from rgknox December 16, 2025 19:27

slevis-lmwg mentioned this pull request Dec 16, 2025

FATES landuse default fluh_timeseries crashes FatesColdLUH test on izumi #2653

Open

Remove FATES_ERROR_EL from user_nl_clm (out-of-scope fix)

25ea275

slevis-lmwg added 3 commits December 17, 2025 13:18

Merge tag 'ctsm5.4.004' into fates-cn

71ed0fe

Update crop parameters and maturity requirements slevis resolved conflicts: src/fates <-- So far I have not changed .gitmodules to point to my branch src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90

Add PRT2 test with synthetic N to replicate the pre-CN-coupling setup

b146c70

slevis-lmwg commented Dec 26, 2025

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Complete the FATES-CLM nitrogen coupling #3409

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