Merge tag 'ctsm5.4.012' into tweaked_ciso_file

Fix for C-balance error that manifested in B-cases with pft 67

Issue ESCOMP#3678
PR ESCOMP#3702

Changes answers more than roundoff (same climate) and occurs rarely.

Author: ekluzek

doc/ChangeLog

@@ -1,4 +1,64 @@
 ===============================================================
+Tag name: ctsm5.4.012
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Mon Jan 26 03:13:02 PM MST 2026
+One-line Summary: Fix C-balance error for partly emerged crops
+
+Purpose and description of changes
+----------------------------------
+
+ In CNPhenology, to the section "plant had emerged before harvest" I added a subsection "plant partly emerged from the ground" that repeats the code from the "else" section just after that's labeled "plant never emerged from the ground."
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #3678
+
+Testing summary:
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+    - Configurations: Four BASELINE tests show DIFFs. Three derecho_intel, one izumi_nag, all four I2000Clm60BgcCrop:
+ ERP_P64x2_Ld765.f10_f10_mg37.I2000Clm60BgcCrop.derecho_intel.clm-monthly BASELINE ctsm5.4.011: DIFF
+ ERS_Ly3.f10_f10_mg37.I2000Clm60BgcCrop.derecho_intel BASELINE ctsm5.4.011: DIFF
+ SMS_Ly2_PS.f19_g17.I2000Clm60BgcCrop.derecho_intel.clm-cropMonthOutput BASELINE ctsm5.4.011: DIFF
+ SMS_D_Ld65.f10_f10_mg37.I2000Clm60BgcCrop.izumi_nag.clm-FireLi2024GSWP BASELINE ctsm5.4.011: DIFF
+    - Nature of change: Potentially larger than roundoff (certainly in B-cases) but same climate and rare.
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/3702
+
+===============================================================
+===============================================================
 Tag name: ctsm5.4.011
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Thu Jan 22 04:01:52 PM MST 2026

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.4.012   slevis 01/26/2026 Fix C-balance error for partly emerged crops
        ctsm5.4.011   slevis 01/22/2026 Merge b4b-dev to master
        ctsm5.4.010     erik 01/21/2026 Update cime to version that changes answers for ERI tests
        ctsm5.4.009   olyson 01/19/2026 Dewpoint Temperature check for bare ground

src/biogeochem/CNPhenologyMod.F90

@@ -2553,6 +2553,24 @@ subroutine CropPhenology(num_pcropp, filter_pcropp                     , &
                if (tlai(p) > 0._r8) then ! plant had emerged before harvest
                   offset_flag(p) = 1._r8
                   offset_counter(p) = dt
+
+                  ! plant partly emerged from the ground
+                  ! Revert planting transfers; this will replenish the crop seed deficit.
+                  ! We subtract from any existing value in crop_seedc_to_leaf /
+                  ! crop_seedn_to_leaf in the event that we enter this block of
+                  ! code soon after the planting transfer originally occurred.
+                  if (leafc_xfer(p) > 0._r8) then
+                     crop_seedc_to_leaf(p) = crop_seedc_to_leaf(p) - leafc_xfer(p) / dt
+                     crop_seedn_to_leaf(p) = crop_seedn_to_leaf(p) - leafn_xfer(p) / dt
+                     leafc_xfer(p) = 0._r8
+                     leafn_xfer(p) = leafc_xfer(p) / leafcn_t_evolving(p)
+                     if (use_c13) then
+                        c13_cnveg_carbonstate_inst%leafc_xfer_patch(p) = 0._r8
+                     endif
+                     if (use_c14) then
+                        c14_cnveg_carbonstate_inst%leafc_xfer_patch(p) = 0._r8
+                     endif
+                  end if
                else                      ! plant never emerged from the ground
                   ! Revert planting transfers; this will replenish the crop seed deficit.
                   ! We subtract from any existing value in crop_seedc_to_leaf /
@@ -2569,7 +2587,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp                     , &
                   if (use_c14) then
                      c14_cnveg_carbonstate_inst%leafc_xfer_patch(p) = 0._r8
                   endif
-
                end if
 
                ! enter phase 3 while previous criteria fail and next is true;