Merge pull request #3777 from slevis-lmwg/merge-b4bdev-20260219

Merge b4bdev 20260219

Author: ekluzek

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -2497,11 +2497,11 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.4.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <stream_fldfilename_urbantv phys="clm6_0" hgrid="0.9x1.25" urban_explicit_ac=".false."
 >lnd/clm2/urbandata/CTSM52_tbuildmax_OlesonFeddema_2020_0.9x1.25_simyr1849-2106_c200605.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm6_0"  hgrid="0.9x1.25" urban_explicit_ac=".true."
->lnd/clm2/urbandata/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+>lnd/clm2/urbandata/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20260217.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25" urban_explicit_ac=".false."
 >lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm5_0" hgrid="0.9x1.25" urban_explicit_ac=".true."
->lnd/clm2/urbandata/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc</stream_fldfilename_urbantv>
+>lnd/clm2/urbandata/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20260217.nc</stream_fldfilename_urbantv>
 <stream_fldfilename_urbantv phys="clm4_5" hgrid="0.9x1.25"
 >lnd/clm2/urbandata/CLM45_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc</stream_fldfilename_urbantv>
 
@@ -2649,7 +2649,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.4.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <use_prigent_roughness dust_emis_method="Leung_2023">.true.</use_prigent_roughness>
 <use_prigent_roughness                              >.false.</use_prigent_roughness>
 <stream_fldfilename_prigentroughness
->lnd/clm2/dustemisdata/Prigent_2005_roughness_0.25x0.25_cdf5_c240127.nc</stream_fldfilename_prigentroughness>
+>lnd/clm2/dustemisdata/Prigent_2005_roughness_0.25x0.25_cdf5_c260218.nc</stream_fldfilename_prigentroughness>
 <stream_meshfile_prigentroughness
 >lnd/clm2/dustemisdata/dust_0.25x0.25_ESMFmesh_cdf5_c240222.nc</stream_meshfile_prigentroughness>
 

cime_config/config_archive.xml

@@ -3,9 +3,10 @@
     <rest_file_extension>r</rest_file_extension>
     <rest_file_extension>rh\da</rest_file_extension>
     <rest_file_extension>rh\di</rest_file_extension>
-    <hist_file_extension>h\d*.*\.nc$</hist_file_extension>
-    <hist_file_extension>lilac_hi.*\.nc$</hist_file_extension>
-    <hist_file_extension>lilac_atm_driver_h\d*.*\.nc$</hist_file_extension>
+    <!-- History files including those for LILAC, optionally include gzipped files which is needed for DART -->
+    <hist_file_extension>h\d*.*\.nc(\.gz)?$</hist_file_extension>
+    <hist_file_extension>lilac_hi.*\.nc(\.gz)?$</hist_file_extension>
+    <hist_file_extension>lilac_atm_driver_h\d*.*\.nc(\.gz)?$</hist_file_extension>
     <hist_file_extension>e</hist_file_extension>
     <rest_history_varname>locfnh</rest_history_varname>
     <rpointer>

doc/ChangeLog

@@ -1,4 +1,114 @@
 ===============================================================
+Tag name: ctsm5.4.021
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Fri Feb 20 08:19:42 PM MST 2026
+One-line Summary: Bring b4b-dev to master
+
+Purpose and description of changes
+----------------------------------
+
+Some fixes to use the ifx compiler. Added handling of gzipped files in the short term archiver
+needed for DART. Use a CMake funciton for the PfUnit build. Make sure mksurfdata_esmf PIO library is
+used as shared in the build. Fix to a typo in the Technical Note.
+
+Use pytest instead of unittest in our python unit test framework, which allows many modern features.
+One test file, test_unit_longitude.py, has been modified to use pytest's "parametrize" functionality as an example. Most of the changed lines in that file are just whitespace differences.
+
+Existing run_ctsm_py_tests arguments have been ported to replicate the same functionality in pytest. Unknown arguments will be passed to pytest directly.
+
+Also: Made it so that the tests can be called from anywhere in the checkout, instead of only python/.
+
+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]:
+
+Resolves #3762 by Bill Sacks ifx issues
+Resolves #3763 by Bill Sacks Floating invalid with ifx
+Resolves #3774 by Erik Kluzek NaN's in Prigent and urbantv streams
+Resolves #3082 by Kevin Raeder st_archive for DART
+Resolves #3616 by Sam Rabin convert python unittests to pytest
+Resolves #3035 by Keith Oleson typo in LW documentation in tech. note
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+   The Short Term archiver can now also save files that are g-zipped
+   This is something that is needed for DART
+
+Changes to the datasets (e.g., streams, surface or initial files):
+    New Prigent and urbantv streams datasets with NaN's removed
+
+Changes to documentation: Fix issue in tech. note
+
+Notes of particular relevance for developers: regular
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   The ctsm_pylib conda environment changed! Rerun py_env_create to update it
+
+Changes to tests or testing:
+   Python unit test framework changed from unittest to pytest. So now pytest functionality can be used
+   in tests
+
+Testing summary: regular
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - OK
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+#3765 Fixes for ifx, from Bill Sacks
+#3084 Added code to make st-archive handle DART files, from Kevin Raeder
+#3761 Use pytest instead of unittest in run_ctsm_py_tests, from Sam Rabin
+#3582 Use a CMake function provided by CIME, from Bill Sacks
+#3700 Fix mksurfdata CMakeLists.txt: use SHARED for .so PIO libraries, from Cooper DeVane-Prugh
+#3220 Tech Note: Distinguish between time step and iteration level in vegetation longwave and fluxes, from Keith Oleson
+
+===============================================================
+===============================================================
 Tag name: ctsm5.4.020
 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
 Date: Thu Feb 19 08:28:59 AM MST 2026

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.4.021     erik 02/20/2026 Bring b4b-dev to master
        ctsm5.4.020   slevis 02/19/2026 Address carbon cycle and fire biases in CESM3 development runs by updating namelist defaults
        ctsm5.4.019 samrabin 02/12/2026 Fix years used by generate_gdds
        ctsm5.4.018     erik 02/12/2026 Quick fix so that we can use Nitrogen Deposition sent from the ATM model

doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst

@@ -1147,7 +1147,7 @@ where :math:`\overrightarrow{S}_{v}` is the solar radiation absorbed by the vege
 
    \Delta T_{v} =\frac{\overrightarrow{S}_{v} -\overrightarrow{L}_{v} -H_{v} -\lambda E_{v} }{\frac{\partial \overrightarrow{L}_{v} }{\partial T_{v} } +\frac{\partial H_{v} }{\partial T_{v} } +\frac{\partial \lambda E_{v} }{\partial T_{v} } }
 
-where :math:`\Delta T_{v} =T_{v}^{n+1} -T_{v}^{n}` and the subscript "n" indicates the iteration.
+where :math:`\Delta T_{v} =T_{v}^{k+1} -T_{v}^{k}` and the subscript "k" indicates the iteration.
 
 The partial derivatives are
 
@@ -1227,9 +1227,9 @@ The numerical solution for vegetation temperature and the fluxes of momentum, se
 
 #. Latent heat flux from vegetation :math:`\lambda E_{v}` (:eq:`5.101` )
 
-#. If the latent heat flux has changed sign from the latent heat flux computed at the previous iteration (:math:`\lambda E_{v} ^{n+1} \times \lambda E_{v} ^{n} <0`), the latent heat flux is constrained to be 10% of the computed value. The difference between the constrained and computed value (:math:`\Delta _{1} =0.1\lambda E_{v} ^{n+1} -\lambda E_{v} ^{n+1}` ) is added to the sensible heat flux later.
+#. If the latent heat flux has changed sign from the latent heat flux computed at the previous iteration (:math:`\lambda E_{v} ^{k+1} \times \lambda E_{v} ^{k} <0`), the latent heat flux is constrained to be 10% of the computed value. The difference between the constrained and computed value (:math:`\Delta _{1} =0.1\lambda E_{v} ^{k+1} -\lambda E_{v} ^{k+1}` ) is added to the sensible heat flux later.
 
-#. Change in vegetation temperature :math:`\Delta T_{v}` (:eq:`5.129` ) and update the vegetation temperature as :math:`T_{v}^{n+1} =T_{v}^{n} +\Delta T_{v}`. :math:`T_{v}` is constrained to change by no more than 1°K in one iteration. If this limit is exceeded, the energy error is
+#. Change in vegetation temperature :math:`\Delta T_{v}` (:eq:`5.129` ) and update the vegetation temperature as :math:`T_{v}^{k+1} =T_{v}^{k} +\Delta T_{v}`. :math:`T_{v}` is constrained to change by no more than 1°K in one iteration. If this limit is exceeded, the energy error is
 
    .. math::
       :label: 5.138
@@ -1269,7 +1269,7 @@ The error :math:`\lambda \Delta _{3}` is added to the sensible heat flux later.
 
 #. Monin-Obukhov length :math:`L` (:eq:`5.49` )
 
-#. The iteration is stopped after two or more steps if :math:`\tilde{\Delta }T_{v} <0.01` and :math:`\left|\lambda E_{v}^{n+1} -\lambda E_{v}^{n} \right|<0.1` where :math:`\tilde{\Delta }T_{v} =\max \left(\left|T_{v}^{n+1} -T_{v}^{n} \right|,\, \left|T_{v}^{n} -T_{v}^{n-1} \right|\right)`, or after forty iterations have been carried out.
+#. The iteration is stopped after two or more steps if :math:`\tilde{\Delta }T_{v} <0.01` and :math:`\left|\lambda E_{v}^{k+1} -\lambda E_{v}^{k} \right|<0.1` where :math:`\tilde{\Delta }T_{v} =\max \left(\left|T_{v}^{k+1} -T_{v}^{k} \right|,\, \left|T_{v}^{k} -T_{v}^{k-1} \right|\right)`, or after forty iterations have been carried out.
 
 #. Momentum fluxes :math:`\tau _{x}`, :math:`\tau _{y}` (:eq:`5.5`, :eq:`5.6`)
 

doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst

@@ -141,9 +141,9 @@ where
 .. math::
    :label: 4.14
 
-   \begin{array}{l} {L_{vg} \, \uparrow =\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\left(1-\varepsilon _{v} \right)L_{atm} \, \downarrow } \\ {\qquad \qquad +\varepsilon _{v} \left[1+\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\right]\sigma \left(T_{v}^{n} \right)^{3} \left[T_{v}^{n} +4\left(T_{v}^{n+1} -T_{v}^{n} \right)\right]} \\ {\qquad \qquad +\varepsilon _{g} \left(1-\varepsilon _{v} \right)\sigma \left(T_{g}^{n} \right)^{4} } \\ {\qquad =\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\left(1-\varepsilon _{v} \right)L_{atm} \, \downarrow } \\ {\qquad \qquad +\varepsilon _{v} \sigma \left(T_{v}^{n} \right)^{4} } \\ {\qquad \qquad +\varepsilon _{v} \left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\sigma \left(T_{v}^{n} \right)^{4} } \\ {\qquad \qquad +4\varepsilon _{v} \sigma \left(T_{v}^{n} \right)^{3} \left(T_{v}^{n+1} -T_{v}^{n} \right)} \\ {\qquad \qquad +4\varepsilon _{v} \left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\sigma \left(T_{v}^{n} \right)^{3} \left(T_{v}^{n+1} -T_{v}^{n} \right)} \\ {\qquad \qquad +\varepsilon _{g} \left(1-\varepsilon _{v} \right)\sigma \left(T_{g}^{n} \right)^{4} } \end{array}
+   \begin{array}{l} {L_{vg} \, \uparrow =\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\left(1-\varepsilon _{v} \right)L_{atm} \, \downarrow } \\ {\qquad \qquad +\varepsilon _{v} \left[1+\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\right]\sigma \left(T_{v}^{n+1,k} \right)^{3} \left[T_{v}^{n+1,k} +4\left(T_{v}^{n+1,k+1} -T_{v}^{n+1,k} \right)\right]} \\ {\qquad \qquad +\varepsilon _{g} \left(1-\varepsilon _{v} \right)\sigma \left(T_{g}^{n} \right)^{4} } \\ {\qquad =\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\left(1-\varepsilon _{v} \right)L_{atm} \, \downarrow } \\ {\qquad \qquad +\varepsilon _{v} \sigma \left(T_{v}^{n+1,k} \right)^{4} } \\ {\qquad \qquad +\varepsilon _{v} \left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\sigma \left(T_{v}^{n+1,k} \right)^{4} } \\ {\qquad \qquad +4\varepsilon _{v} \sigma \left(T_{v}^{n+1,k} \right)^{3} \left(T_{v}^{n+1,k+1} -T_{v}^{n+1,k} \right)} \\ {\qquad \qquad +4\varepsilon _{v} \left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\sigma \left(T_{v}^{n+1,k} \right)^{3} \left(T_{v}^{n+1,k+1} -T_{v}^{n+1,k} \right)} \\ {\qquad \qquad +\varepsilon _{g} \left(1-\varepsilon _{v} \right)\sigma \left(T_{g}^{n} \right)^{4} } \end{array}
 
-where :math:`\varepsilon _{v}` is the vegetation emissivity and :math:`T_{v}^{n+1}` and :math:`T_{v}^{n}` are the vegetation temperatures at the current and previous time steps, respectively (:ref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`). The first term in the equation above is the atmospheric longwave radiation that is transmitted through the canopy, reflected by the ground, and transmitted through the canopy to the atmosphere. The second term is the longwave radiation emitted by the canopy directly to the atmosphere. The third term is the longwave radiation emitted downward from the canopy, reflected by the ground, and transmitted through the canopy to the atmosphere. The fourth term is the increase (decrease) in longwave radiation due to an increase (decrease) in canopy temperature that is emitted by the canopy directly to the atmosphere. The fifth term is the increase (decrease) in longwave radiation due to an increase (decrease) in canopy temperature that is emitted downward from the canopy, reflected from the ground, and transmitted through the canopy to the atmosphere. The last term is the longwave radiation emitted by the ground and transmitted through the canopy to the atmosphere.
+where :math:`\varepsilon _{v}` is the vegetation emissivity, :math:`T_{v}^{n+1,k+1}` and :math:`T_{v}^{n+1,k}` are the vegetation temperatures at the current time step and current and previous iteration, respectively, where :math:`k` is the iteration level (:ref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`). The first term in the equation above is the atmospheric longwave radiation that is transmitted through the canopy, reflected by the ground, and transmitted through the canopy to the atmosphere. The second term is the longwave radiation emitted by the canopy directly to the atmosphere. The third term is the longwave radiation emitted downward from the canopy, reflected by the ground, and transmitted through the canopy to the atmosphere. The fourth term is the increase (decrease) in longwave radiation due to an increase (decrease) in canopy temperature that is emitted by the canopy directly to the atmosphere. The fifth term is the increase (decrease) in longwave radiation due to an increase (decrease) in canopy temperature that is emitted downward from the canopy, reflected from the ground, and transmitted through the canopy to the atmosphere. The last term is the longwave radiation emitted by the ground and transmitted through the canopy to the atmosphere.
 
 The upward longwave radiation from the ground is
 
@@ -157,7 +157,7 @@ where :math:`L_{v} \, \downarrow` is the downward longwave radiation below the v
 .. math::
    :label: 4.16
 
-   L_{v} \, \downarrow =\left(1-\varepsilon _{v} \right)L_{atm} \, \downarrow +\varepsilon _{v} \sigma \left(T_{v}^{n} \right)^{4} +4\varepsilon _{v} \sigma \left(T_{v}^{n} \right)^{3} \left(T_{v}^{n+1} -T_{v}^{n} \right).
+   L_{v} \, \downarrow =\left(1-\varepsilon _{v} \right)L_{atm} \, \downarrow +\varepsilon _{v} \sigma \left(T_{v}^{n+1,k} \right)^{4} +4\varepsilon _{v} \sigma \left(T_{v}^{n+1,k} \right)^{3} \left(T_{v}^{n+1,k+1} -T_{v}^{n+1,k} \right).
 
 The net longwave radiation flux for the ground is (positive toward the atmosphere)
 

python/Makefile

@@ -28,10 +28,6 @@ PYLINT_SRC = \
 #       ../cime_config/buildnml
 
 all: test black lint
-# ----------------------------------------------------------------
-# See the stest target about this issue
-	@echo "Run './run_ctsm_py_tests --sys' by hand afterwards"
-# ----------------------------------------------------------------
 	@echo
 	@echo
 	@echo "Successfully ran all standard tests"
@@ -45,13 +41,7 @@ utest: FORCE
 .PHONY: stest
 stest: FORCE
 # ----------------------------------------------------------------
-# EBK 2024-03-19: Comment out running here because of this issue:
-# https://github.com/ESCOMP/CTSM/pull/2363#issuecomment-1967884908
-#$(PYTHON) ./run_ctsm_py_tests $(TEST_ARGS) --sys
-# Instead run by hand which seems to be working for now...
-# ----------------------------------------------------------------
-	@echo "System tests currently don't run under Make so..."
-	@echo "Run './run_ctsm_py_tests --sys' by hand afterwards"
+	$(PYTHON) ./run_ctsm_py_tests $(TEST_ARGS) --sys
 
 .PHONY: lint
 lint: FORCE