Fixes

gold2718 · Oct 29, 2024 · e00f8b1 · e00f8b1
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diff --git a/.gitmodules b/.gitmodules
@@ -1,78 +1,106 @@
+# This is a git submodule file with additional support for
+# git-fleximod (https://github.com/ESMCI/git-fleximod)
+#
+# The additional flags supported by git-fleximod are
+# fxtag - the tag associated with the submodule, this tag can be tested for
+#         consistancy with the submodule hash using git-fleximod status
+#         the hash can be updated to the tag using git-fleximod update
+#
+# fxrequired - indicates if a given submodule should be checked out on install
+#              submoudules can be toplevel or internal and required or optional
+#              toplevel means that the submodule should only be checked out if the
+#              module is the toplevel of the git repo (is not a submodule itself)
+#              internal means that the submodule is needed by the component whether
+#              the component is toplevel or the submodule of another repo
+#              required means that the submodule should always be checked out
+#              optional means that the submodule should only be checked out if the
+#              optional flag is provided to git-fleximod or the submodule name is
+#              explicitly listed on the git-fleximod command line.
+#
+# fxsparse -   this is a path to a git sparse checkout file indicating that the
+#              submodule should be checked out in sparse mode
+#
+# fxDONOTUSEurl    -   this field is used by git-fleximod test to insure that the url is pointing
+#              to the official url of the repo and not to an unofficial fork.
+#              It is intended for use of github workflows to test commits to protected
+#              repository branches.
+#
+
 #-----------------------------
 # Required CAM externals
 #-----------------------------
 
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/ESCOMP/atmospheric_physics
-        fxtag = atmos_phys0_05_001
-        fxrequired = AlwaysRequired
+	fxtag = atmos_phys0_06_009
+	fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
 [submodule "chem_proc"]
 	path = chem_proc
 	url = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
-        fxrequired = AlwaysRequired
-        fxtag = chem_proc5_0_06
+	fxtag = chem_proc5_0_06
+	fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
 
 [submodule "carma"]
 	path = src/physics/carma/base
 	url = https://github.com/ESCOMP/CARMA_base.git
-        fxrequired = AlwaysRequired
-        fxtag = carma4_01
-        fxDONOTUSEurl = https://github.com/ESCOMP/CARMA_base.git
+	fxtag = carma4_01
+	fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/ESCOMP/CARMA_base.git
 
 [submodule "clubb"]
 	path = src/physics/clubb
 	url = https://github.com/larson-group/clubb_release
-        fxrequired = AlwaysRequired
-        fxsparse = ../.clubb_sparse_checkout
-        fxtag = clubb_4ncar_20240605_73d60f6_gpufixes_posinf
-        fxDONOTUSEurl = https://github.com/larson-group/clubb_release
+	fxtag = clubb_4ncar_20240605_73d60f6_gpufixes_posinf
+	fxsparse = ../.clubb_sparse_checkout
+	fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/larson-group/clubb_release
 
 [submodule "cosp2"]
 	path = src/physics/cosp2/src
 	url = https://github.com/CFMIP/COSPv2.0
-        fxrequired = AlwaysRequired
-        fxsparse = ../.cosp_sparse_checkout
-        fxtag = v2.1.4cesm
+	fxtag = v2.1.4cesm
+	fxsparse = ../.cosp_sparse_checkout
+	fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/CFMIP/COSPv2.0
 
 [submodule "hemco"]
 	path = src/hemco
 	url = https://github.com/ESCOMP/HEMCO_CESM.git
-        fxtag = hemco-cesm2_0_hemco3_9_0
-        fxrequired = AlwaysRequired
+	fxtag = hemco-cesm2_0_hemco3_9_0
+	fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/HEMCO_CESM.git
 
 [submodule "pumas"]
 	path = src/physics/pumas
 	url = https://github.com/ESCOMP/PUMAS
-        fxrequired = AlwaysRequired
-        fxtag = pumas_cam-release_v1.36
-        fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
+	fxtag = pumas_cam-release_v1.36
+	fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
 
 [submodule "pumas-frozen"]
 	path = src/physics/pumas-frozen
 	url = https://github.com/ESCOMP/PUMAS
-        fxrequired = AlwaysRequired
-        fxtag = pumas_cam-release_v1.17_rename
-        fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
+	fxtag = pumas_cam-release_v1.17_rename
+	fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
 
 [submodule "rrtmgp-data"]
 	path = src/physics/rrtmgp/data
 	url = https://github.com/earth-system-radiation/rrtmgp-data.git
-        fxrequired = AlwaysRequired
-        fxtag = v1.8
-        fxDONOTUSEurl = https://github.com/earth-system-radiation/rrtmgp-data.git
+	fxtag = v1.8
+	fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/earth-system-radiation/rrtmgp-data.git
 
 [submodule "rte-rrtmgp"]
 	path = src/physics/rrtmgp/ext
 	url = https://github.com/earth-system-radiation/rte-rrtmgp.git
-        fxrequired = AlwaysRequired
-        fxtag = v1.7
-        fxDONOTUSEurl = https://github.com/earth-system-radiation/rte-rrtmgp.git
+	fxtag = v1.7
+	fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/earth-system-radiation/rte-rrtmgp.git
 
 #-----------------------------
 # Optional CAM externals
@@ -81,37 +109,37 @@
 [submodule "ali_arms"]
 	path = src/physics/ali_arms
 	url = https://github.com/ESCOMP/ALI-ARMS
-        fxrequired = AlwaysOptional
-        fxtag = ALI_ARMS_v1.0.1
-        fxDONOTUSEurl = https://github.com/ESCOMP/ALI-ARMS
+	fxtag = ALI_ARMS_v1.0.1
+	fxrequired = AlwaysOptional
+	fxDONOTUSEurl = https://github.com/ESCOMP/ALI-ARMS
 
 [submodule "cloud_j"]
 	path = src/chemistry/cloud_j
 	url = https://github.com/geoschem/cloud-j.git
-        fxrequired = AlwaysOptional
-        fxtag = 7.7.3
-        fxDONOTUSEurl = https://github.com/geoschem/cloud-j.git
+	fxtag = 7.7.3
+	fxrequired = AlwaysOptional
+	fxDONOTUSEurl = https://github.com/geoschem/cloud-j.git
 
 [submodule "geoschem"]
 	path = src/chemistry/geoschem/geoschem_src
 	url = https://github.com/geoschem/geos-chem.git
-        fxrequired = AlwaysOptional
-        fxtag = 14.4.3
-        fxDONOTUSEurl = https://github.com/geoschem/geos-chem.git
+	fxtag = 14.4.3
+	fxrequired = AlwaysOptional
+	fxDONOTUSEurl = https://github.com/geoschem/geos-chem.git
 
 [submodule "hetp"]
 	path = src/chemistry/hetp
 	url = https://github.com/geoschem/heterogeneous-vectorized-or-parallel.git
-        fxrequired = AlwaysOptional
-        fxtag = geoschem_hetp_1.0
-        fxDONOTUSEurl = https://github.com/geoschem/heterogeneous-vectorized-or-parallel.git
+	fxtag = geoschem_hetp_1.0
+	fxrequired = AlwaysOptional
+	fxDONOTUSEurl = https://github.com/geoschem/heterogeneous-vectorized-or-parallel.git
 
 [submodule "mpas"]
 	path = src/dynamics/mpas/dycore
 	url = https://github.com/MPAS-Dev/MPAS-Model.git
-        fxrequired = AlwaysOptional
-        fxsparse = ../.mpas_sparse_checkout
-        fxtag = v8.2.1
+	fxtag = v8.2.1
+	fxsparse = ../.mpas_sparse_checkout
+	fxrequired = AlwaysOptional
 	fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
 
 #-----------------------------
@@ -175,7 +203,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 [submodule "cice6"]
 path = components/cice
 url = https://github.com/NorESMhub/NorESM_CICE
-fxtag = cesm_cice6_5_0_20240702_noresm_v1
+fxtag = cesm_cice6_5_0_20240702_noresm_v2
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NorESMhub/NorESM_CICE
 

diff --git a/bld/config_files/definition.xml b/bld/config_files/definition.xml
@@ -57,8 +57,8 @@ Option to turn on waccmx thermosphere/ionosphere extension: 0 => no, 1 => yes
 <entry id="ionosphere" valid_values="none,wxie" value="none">
 Ionosphere model used in WACCMX.
 </entry>
-<entry id="phys" valid_values="cam3,cam4,cam5,cam6,cam_dev,held_suarez,adiabatic,kessler,tj2016,grayrad,spcam_sam1mom,spcam_m2005" value="">
-Physics package: cam3, cam4, cam5, cam6, cam_dev, held_suarez, adiabatic, kessler, tj2016, grayrad, spcam_sam1mom, spcam_m2005.
+<entry id="phys" valid_values="cam3,cam4,cam5,cam6,cam7,held_suarez,adiabatic,kessler,tj2016,grayrad,spcam_sam1mom,spcam_m2005" value="">
+Physics package: cam3, cam4, cam5, cam6, cam7, held_suarez, adiabatic, kessler, tj2016, grayrad, spcam_sam1mom, spcam_m2005.
 </entry>
 <entry id="hemco" valid_values="0,1" value="0">
 Switch to turn on Harmonized Emissions Component (HEMCO) for chemistry: 0 => no, 1 => yes.
@@ -153,9 +153,13 @@ Modifications that allow perturbation growth testing: 0=off, 1=on.
 Configure CAM for single column mode: 0=off, 1=on.  This option only
 supported for the Eulerian dycore.
 </entry>
+<entry id="scam_iop" valid_values="arm95,arm97,atex,bomex,cgilss11,cgilss12,cgilss6,dycomsrf01,dycomsrf02,gateiii,mpace,rico,sas,sparticus,togaii,twp06,camfrc,none" value="none">
+Single column IOP
+Supported for Eulerian and SE dycores.
+</entry>
 <entry id="camiop" valid_values="0,1" value="0">
 Configure CAM to generate an IOP file that can be used to drive SCAM: 0=no, 1=yes.
-This option only supported for the Eulerian dycore.
+This option supported for the Eulerian and SE dycores.
 </entry>
 <entry id="hgrid" value="">
 Horizontal grid specifier.  The recognized values depend on

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -8,11 +8,11 @@
       CAM
     ===============
    -->
-    <desc atm="CAM70[%LT][%MT][%CT1S][%CT4S]"                                                                                                                                                                                                                                                                                                                                            >CAM cam7 physics:</desc>
+    <desc atm="CAM70[%LT][%MT][%CT1S][%CT4S][%GHGMAM4][%NORESM][%TROPMAM4][%CAMoslo]"                                                                                                                                                                                                                                                                                                    >CAM cam7 physics:</desc>
     <desc atm="CAM60[%1PCT][%4xCO2][%CT1S][%CT2S][%CFIRE][%CVBSX][%NUDG][%PORT][%RCO2][%SCAM][%SDYN][%WCCM][%WCMD][%WCSC][%WCTS][%WXIE][%WXIED][%HEMCO][%GEOSCHEM][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]" >CAM cam6 physics:</desc>
     <desc atm="CAM50[%CT1S][%CLB][%PORT][%RCO2][%MAM7][%SCAM][%SDYN][%WCSC][%WCTS][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]"                                                                                 >CAM cam5 physics:</desc>
     <desc atm="CAM40[%PORT][%RCO2][%SCAM][%SDYN][%TMOZ][%WX][%WXIE][%WXIED][%WCCM][%WCMD][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]"                                                                          >CAM cam4 physics:</desc>
-    <desc atm="CAM[%ADIAB][%DABIP04][%TJ16][%GRAYRAD][%HS94][%KESSLER][%RCO2][%SPCAMS][%SPCAMCLBS][%SPCAMM][%SPCAMCLBM]"                                     >CAM simplified and non-versioned physics :</desc>
+    <desc atm="CAM[%ADIAB][%DABIP04][%TJ16][%GRAYRAD][%HS94][%KESSLER][%RCO2][%SPCAMS][%SPCAMCLBS][%SPCAMM][%SPCAMCLBM]"                                                                                                                                                                                                                                                                 >CAM simplified and non-versioned physics :</desc>
 
     <!--
         =================
@@ -43,13 +43,14 @@
      CAM Options
     ===============
    -->
+    <desc option="CFIRE"        >CAM-Chem troposphere/stratosphere chem with simplified volatility basis set SOA scheme and fire emissons :</desc>
+    <desc option="CLB"          >CAM CLUBB - turned on by default in CAM60:</desc>
     <desc option="CT1S"         >CAM-Chem troposphere/stratosphere chemistry with simplified VBS-SOA:</desc>
     <desc option="CT2S"         >CAM-Chem troposphere/stratosphere chemistry with simplified VBS-SOA and expanded isoprene and terpene oxidation:</desc>
     <desc option="CT4S"         >CAM-Chem troposphere/stratosphere simplified chemistry for climate simulations:</desc>
-    <desc option="GEOSCHEM"     >GEOS-Chem troposphere/stratosphere chemistry :</desc>
-    <desc option="CFIRE"        >CAM-Chem troposphere/stratosphere chem with simplified volatility basis set SOA scheme and fire emissons :</desc>
-    <desc option="CLB"          >CAM CLUBB - turned on by default in CAM60:</desc>
     <desc option="CVBSX"        >CAM-Chem troposphere/stratosphere chem with extended volatility basis set SOA scheme and modal aersols :</desc>
+    <desc option="GEOSCHEM"     >GEOS-Chem troposphere/stratosphere chemistry :</desc>
+    <desc option="GHGMAM4"      >Prognostic GHG chemistry mechanism for CAM7:</desc>
     <desc option="LT"           >CAM low top model </desc>
     <desc option="MAM7"         >Modal Aerosol Model composed of 7 modes: </desc>
     <desc option="MT"           >CAM mid top model </desc>
@@ -153,10 +154,12 @@
       <!-- NorESM-specific modifiers -->
       <value compset="_CAM.*(%NORESM)">-camnor</value>
       <value compset="_CAM.*(%TROPMAM4)">-chem trop_mam4</value>
+      <value compset="_CAM.*(%GHGMAM4)">-chem ghg_mam4</value>
       <value compset="_CAM.*(%CAMoslo)">-chem trop_mam_oslo</value>
 
       <!-- Modifiers for CAM runs (%.* includes SCAM runs) -->
       <value compset="_CAM.*(%CT1S|%CFIRE)">-chem trop_strat_mam5_vbs</value>
+      <value compset="_CAM.*(%GHGMAM4)">-chem ghg_mam4</value>
       <value compset="_CAM60.*%(GEOSCHEM)">-chem geoschem_mam4</value>
 
       <value compset="%MAM7">-chem trop_mam7</value>
@@ -341,10 +344,11 @@
       <value compset="CAM%KESSLER"       >dctest_baro_kessler</value>
 
       <!-- NorESM use cases -->
+      <value compset="1850_CAM70%LT%NORESM%TROPMAM4" >1850_camnor_lt_tropmam4</value>
+      <value compset="1850_CAM70%LT%NORESM%CAMoslo"  >1850_camnor_lt_osloaero</value>
       <value compset="HIST_CAM70%LT%NORESM%TROPMAM4">hist_camnor_lt_tropmam4</value>
       <value compset="HIST_CAM70%LT%NORESM%CAMoslo" >hist_camnor_lt_osloaero</value>
 
-
       <!-- SCAM defaults to ARM97, all other IOPs are in usermods_dirs -->
       <!--       <value compset="CAM[456]0%SCAM"    >scam_arm97</value> -->
     </values>

diff --git a/components/mizuRoute b/components/mizuRoute
diff --git a/components/rtm b/components/rtm
diff --git a/src/atmos_phys b/src/atmos_phys