ctsm5.4.036: 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

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.

ekluzek

I did a fairly quick skim, and only have a few suggestions. There was one thing I was concerned about, but realized it was done on purpose. So I only wonder if more comments might help with the supplemental nitrogen setting?

@glemieux had some comments to handle. And we should have him and @samsrabin finish a review as well.

The other thing I wondered about this is how FATES carbon_nitrogen will interact with other parts of Nitrogen in CLM like LUNA? That likely will take some scientific validation, but we might want to have some warnings or comments about some of that?

ekluzek · 2026-04-22T17:41:37Z


+<!-- Supplmental Nitrogen mode -->
+<suplnitro >NONE</suplnitro>
+<suplnitro fates_parteh_mode="carbon_only" >ALL</suplnitro>


Doesn't this need the addition of:

Suggested change

<suplnitro fates_parteh_mode="carbon_only" >ALL</suplnitro>

<suplnitro use_fates=".true." >ALL</suplnitro>

<suplnitro use_fates=".true." fates_parteh_mode="carbon_only" >ALL</suplnitro>

OK, it looks like this was an intentional change. I only wonder about making this more obvious in comments though.

ekluzek · 2026-04-22T17:44:17Z

-  integer, public            :: fates_parteh_mode = -9                  ! 1 => carbon only
-                                                                        ! 2 => C+N+P (not enabled yet)
-                                                                        ! no others enabled
+  character(len=256), public :: fates_parteh_mode = ''                  ! FATES Plant Allocation Reactions and Transport Hypotheses


I really love upgrading this to a character description. So much easier to understand!

ekluzek · 2026-04-22T17:50:47Z


-<entry id="fates_parteh_mode" type="integer" category="physics"
-        group="clm_inparm" valid_values="1,2">
+<entry id="fates_parteh_mode" type="char*256" category="physics"


You could make the string shorter. If you use SHR_KIND_CS it would be 80 characters which is still longer than needed for this. But, you could use it in the code and have it consistent here.

Suggested change

<entry id="fates_parteh_mode" type="char*256" category="physics"

<entry id="fates_parteh_mode" type="char*256" category="physics"

ekluzek · 2026-04-22T17:56:36Z

-  integer, public            :: fates_parteh_mode = -9                  ! 1 => carbon only
-                                                                        ! 2 => C+N+P (not enabled yet)
-                                                                        ! no others enabled
+  character(len=256), public :: fates_parteh_mode = ''                  ! FATES Plant Allocation Reactions and Transport Hypotheses


I do suggest either hardcoding the length to something shorter (and agree with the value in the namelist defintion above), or use SHR_KIND_CS which has a length of 80.

You can add a use statement to shr_kind, for it, and then use it similar to other string lengths.

Suggested change

character(len=256), public :: fates_parteh_mode = '' ! FATES Plant Allocation Reactions and Transport Hypotheses

character(len=CS), public :: fates_parteh_mode = '' ! FATES Plant Allocation Reactions and Transport Hypotheses

use shr_kind_mod, only: CS=>SHR_KIND_CS

ekluzek · 2026-04-22T17:59:30Z

            end do
         end do

+         bgc_soilc_loop2: do fc = 1, num_bgc_soilc


Add a comment to say what this loop is doing.

ekluzek · 2026-04-22T18:12:23Z

+<entry id="fates_parteh_mode" type="char*256" category="physics"
+       group="clm_inparm" valid_values="carbon_only,carbon_nitrogen">
 Switch deciding which nutrient model to use in FATES.
 (Only relevant if FATES is on)


The other thing I wonder about is making a note to say that this is experimental.

Suggested change

(Only relevant if FATES is on)

(Only relevant if FATES is on)

(fates_parteh_mode='carbon_nitrogen' is EXPERIMENTAL and UNSUPPORTED)

rosiealice · 2026-04-22T23:17:20Z

Hi @ekluzek thanks for this. I just wanted to say that this code does not intersect with LUNA, as Vcmax is an input oarameter in FATES and so we don't for now handle any of the acclimation processes that LUNA predicts. This also goes for FUN and the 'Flex-CN' (I'm unsure if we still call it that) functionality.

slevis-lmwg · 2026-04-23T15:54:39Z

Note to self: Open new documentation issues to update Technote and User's Guide.

slevis-lmwg · 2026-04-23T16:24:14Z

Blocked by NGEET/fates#1472 for now.

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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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 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

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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

ekluzek changed the title ~~Complete the FATES-CLM nitrogen coupling~~ ctsm5.4.035: Complete the FATES-CLM nitrogen coupling Apr 22, 2026

ekluzek approved these changes Apr 22, 2026

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ekluzek reviewed Apr 22, 2026

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slevis-lmwg changed the title ~~ctsm5.4.035: Complete the FATES-CLM nitrogen coupling~~ ctsm5.4.036: Complete the FATES-CLM nitrogen coupling Apr 23, 2026

samsrabin changed the title ~~ctsm5.4.036: Complete the FATES-CLM nitrogen coupling~~ ctsm5.4.037: Complete the FATES-CLM nitrogen coupling Apr 23, 2026

samsrabin changed the title ~~ctsm5.4.037: Complete the FATES-CLM nitrogen coupling~~ ctsm5.4.036: Complete the FATES-CLM nitrogen coupling Apr 23, 2026

slevis-lmwg added the blocked: dependency Wait to work on this until dependency is resolved label Apr 23, 2026

	<suplnitro fates_parteh_mode="carbon_only" >ALL</suplnitro>
	<suplnitro use_fates=".true." >ALL</suplnitro>
	<suplnitro use_fates=".true." fates_parteh_mode="carbon_only" >ALL</suplnitro>

	<entry id="fates_parteh_mode" type="char*256" category="physics"
	<entry id="fates_parteh_mode" type="char*256" category="physics"

	character(len=256), public :: fates_parteh_mode = '' ! FATES Plant Allocation Reactions and Transport Hypotheses
	character(len=CS), public :: fates_parteh_mode = '' ! FATES Plant Allocation Reactions and Transport Hypotheses

	(Only relevant if FATES is on)
	(Only relevant if FATES is on)
	(fates_parteh_mode='carbon_nitrogen' is EXPERIMENTAL and UNSUPPORTED)

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