Merge tag 'cmeps0.14.50' into dust_emis_mod

cmeps0.14.50

.github/workflows/extbuild.yml

@@ -20,11 +20,11 @@ jobs:
       CPPFLAGS: "-I/usr/include -I/usr/local/include"
 
       # Versions of all dependencies can be updated here
-      ESMF_VERSION: v8.4.2
+      ESMF_VERSION: v8.6.0
       PNETCDF_VERSION: checkpoint.1.12.3
-      NETCDF_FORTRAN_VERSION: v4.6.0
-      PIO_VERSION: pio2_6_0
-      CDEPS_VERSION: cdeps1.0.15
+      NETCDF_FORTRAN_VERSION: v4.6.1
+      PIO_VERSION: pio2_6_2
+      CDEPS_VERSION: cdeps1.0.26
     steps:
       - uses: actions/checkout@v3
         # Build the ESMF library, if the cache contains a previous build
@@ -84,7 +84,7 @@ jobs:
           ref: ${{ env.CDEPS_VERSION }}
       - name: Build CDEPS
         if: steps.cache-cdeps.outputs.cache-hit != 'true'
-        uses: ESCOMP/CDEPS/.github/actions/[email protected].15
+        uses: ESCOMP/CDEPS/.github/actions/[email protected].26
         with:
           esmfmkfile: $HOME/ESMF/lib/libg/Linux.gfortran.64.openmpi.default/esmf.mk
           pio_path: $HOME/pio
@@ -102,6 +102,6 @@ jobs:
           make VERBOSE=1
           popd
 
-      - name: Setup tmate session
-        if: ${{ failure() }}
-        uses: mxschmitt/action-tmate@v3
+#      - name: Setup tmate session
+#        if: ${{ failure() }}
+#        uses: mxschmitt/action-tmate@v3

.github/workflows/srt.yml

@@ -26,8 +26,8 @@ jobs:
       CPPFLAGS: "-I/usr/include -I/usr/local/include "
       LDFLAGS: "-L/usr/lib/x86_64-linux-gnu -lnetcdf -lnetcdff -lpnetcdf"     
       # Versions of all dependencies can be updated here
-      ESMF_VERSION: v8.5.0
-      PARALLELIO_VERSION: pio2_6_0
+      ESMF_VERSION: v8.6.0
+      PARALLELIO_VERSION: pio2_6_2
       CIME_MODEL: cesm
       CIME_DRIVER: nuopc
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -80,7 +80,17 @@ jobs:
         run: |
           pushd cesm
           ./manage_externals/checkout_externals ccs_config cdeps cime share mct cpl7 parallelio
-          
+          cd ccs_config
+          git checkout main
+          cd ../cime
+          git checkout master
+          if [[ ! -e "${PWD}/.gitmodules.bak" ]]
+             then
+              echo "Convering [email protected] to https://github.com urls in ${PWD}/.gitmodules"
+
+              sed -i".bak" "s/[email protected]:/https:\/\/github.com\//g" "${PWD}/.gitmodules"
+          fi
+          git submodule update --init
       - name: Cache ESMF
         id: cache-esmf
         uses: actions/cache@v3

cesm/flux_atmocn/shr_flux_mod.F90

@@ -133,15 +133,18 @@ end subroutine shr_flux_adjust_constants
   !                   Thomas Toniazzo (Bjerknes Centre, Bergen) ”
   !===============================================================================
   SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
-       &               qbot  ,s16O  ,sHDO  ,s18O  ,rbot,  &
+       &               qbot,  rainc ,s16O  ,sHDO  ,s18O  ,rbot,  &
        &               tbot  ,us    ,vs,  pslv,  &
        &               ts    ,mask  , seq_flux_atmocn_minwind, &
        &               sen   ,lat   ,lwup  ,   &
        &               r16O, rhdo, r18O, &
        &               evap  ,evap_16O, evap_HDO, evap_18O, &
        &               taux  ,tauy  ,tref  ,qref  ,   &
        &               ocn_surface_flux_scheme, &
-       &               duu10n,  ustar_sv ,re_sv ,ssq_sv,   &
+       &               add_gusts, & 
+       &               duu10n, & 
+       &               ugust_out, & 
+       &               ustar_sv ,re_sv ,ssq_sv,   &
        &               missval)
 
     ! !USES:
@@ -156,11 +159,13 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
     integer(IN),intent(in) :: nMax        ! data vector length
     integer(IN),intent(in) :: mask (nMax) ! ocn domain mask       0 <=> out of domain
     integer(IN),intent(in) :: ocn_surface_flux_scheme
+    logical ,intent(in)    :: add_gusts
     real(R8)   ,intent(in) :: zbot (nMax) ! atm level height      (m)
     real(R8)   ,intent(in) :: ubot (nMax) ! atm u wind            (m/s)
     real(R8)   ,intent(in) :: vbot (nMax) ! atm v wind            (m/s)
     real(R8)   ,intent(in) :: thbot(nMax) ! atm potential T       (K)
     real(R8)   ,intent(in) :: qbot (nMax) ! atm specific humidity (kg/kg)
+    real(R8)   ,intent(in) :: rainc(nMax) ! atm precip for convective gustiness (kg/m^3) - RBN 24Nov2008/MDF 31Jan2022
     real(R8)   ,intent(in) :: s16O (nMax) ! atm H216O tracer conc. (kg/kg)
     real(R8)   ,intent(in) :: sHDO (nMax) ! atm HDO tracer conc.  (kg/kg)
     real(R8)   ,intent(in) :: s18O (nMax) ! atm H218O tracer conc. (kg/kg)
@@ -188,6 +193,7 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
     real(R8),intent(out)  ::  tref (nMax) ! diag:  2m ref height T     (K)
     real(R8),intent(out)  ::  qref (nMax) ! diag:  2m ref humidity (kg/kg)
     real(R8),intent(out)  :: duu10n(nMax) ! diag: 10m wind speed squared (m/s)^2
+    real(R8),intent(out)  :: ugust_out(nMax) ! diag: gustiness addition to U10 (m/s)
 
     real(R8),intent(out),optional :: ustar_sv(nMax) ! diag: ustar
     real(R8),intent(out),optional :: re_sv   (nMax) ! diag: sqrt of exchange coefficient (water)
@@ -257,14 +263,16 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
     real(R8)    :: tdiff(nMax)               ! tbot - ts
     real(R8)    :: vscl
 
+    real(R8)    :: ugust      ! function: gustiness as a function of convective rainfall.  
+    real(R8)    :: gprec   ! convective rainfall argument for ugust
 
     qsat(Tk)   = 640380.0_R8 / exp(5107.4_R8/Tk)
 
     ! Large and Yeager 2009
     cdn(Umps)  =  0.0027_R8 / min(33.0000_R8,Umps) + 0.000142_R8 + &
          0.0000764_R8 * min(33.0000_R8,Umps) - 3.14807e-13_r8 * min(33.0000_R8,Umps)**6
     ! Capped Large and Pond by wind
-    !   cdn(Umps)  =   0.0027_R8 / min(30.0_R8,Umps) + 0.000142_R8 + 0.0000764_R8 * min(30.0_R8,Umps) 
+    !   cdn(Umps)  =   0.0027_R8 / min(30.0_R8,Umps) + 0.000142_R8 + 0.0000764_R8 * min(30.0_R8,Umps)
     ! Capped Large and Pond by Cd
     !   cdn(Umps) = min(0.0025_R8, (0.0027_R8 / Umps + 0.000142_R8 + 0.0000764_R8 * Umps ))
     ! Large and Pond
@@ -273,6 +281,13 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
     psimhu(xd) = log((1.0_R8+xd*(2.0_R8+xd))*(1.0_R8+xd*xd)/8.0_R8) - 2.0_R8*atan(xd) + 1.571_R8
     psixhu(xd) = 2.0_R8 * log((1.0_R8 + xd*xd)/2.0_R8)
 
+    ! Convective gustiness appropriate for input precipitation.
+    ! Following Regelsperger et al. (2000, J. Clim)
+    ! Ug = log(1.0+6.69R-0.476R^2)
+    ! Coefficients X by 8640 for mm/s (from cam) -> cm/day (for above forumla)
+    ugust(gprec) = log(1._R8+57801.6_r8*gprec-3.55332096e7_r8*(gprec**2))
+
+
     !--- formats ----------------------------------------
     character(*),parameter :: subName = '(flux_atmOcn) '
     character(*),parameter ::   F00 = "('(flux_atmOcn) ',4a)"
@@ -327,7 +342,14 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
           if (mask(n) /= 0) then
 
              !--- compute some needed quantities ---
-             vmag   = max(seq_flux_atmocn_minwind, sqrt( (ubot(n)-us(n))**2 + (vbot(n)-vs(n))**2) )
+             if (add_gusts) then 
+                vmag   = max(seq_flux_atmocn_minwind, sqrt( (ubot(n)-us(n))**2 + (vbot(n)-vs(n))**2) + ugust(min(rainc(n),6.94444e-4_r8)) )
+                ugust_out(n) = ugust(min(rainc(n),6.94444e-4_r8))
+             else 
+                vmag   = max(seq_flux_atmocn_minwind, sqrt( (ubot(n)-us(n))**2 + (vbot(n)-vs(n))**2) )
+                ugust_out(n) = 0.0_r8
+             end if
+
              if (use_coldair_outbreak_mod) then
                 ! Cold Air Outbreak Modification:
                 ! Increase windspeed for negative tbot-ts
@@ -462,6 +484,7 @@ SUBROUTINE flux_atmOcn(logunit, nMax  ,zbot  ,ubot  ,vbot  ,thbot ,   &
              tref  (n) = spval  !  2m reference height temperature (K)
              qref  (n) = spval  !  2m reference height humidity (kg/kg)
              duu10n(n) = spval  ! 10m wind speed squared (m/s)^2
+             ugust_out(n) = spval ! gustiness addition (m/s) 
 
              if (present(ustar_sv)) ustar_sv(n) = spval
              if (present(re_sv   )) re_sv   (n) = spval

cime_config/buildnml

@@ -15,6 +15,7 @@ from CIME.case import Case
 from CIME.nmlgen import NamelistGenerator
 from CIME.utils import expect
 from CIME.utils import get_model, get_time_in_seconds, get_timestamp
+from CIME.namelist import literal_to_python_value
 from CIME.buildnml import create_namelist_infile, parse_input
 from CIME.XML.files import Files
 
@@ -105,7 +106,8 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     config["COMP_OCN"] = case.get_value("COMP_OCN")
     config["COMP_ROF"] = case.get_value("COMP_ROF")
     config["COMP_WAV"] = case.get_value("COMP_WAV")
-
+    config["CAMDEV"] = "True" if "CAM%DEV" in case.get_value("COMPSET") else "False"
+
     if (
         (
             case.get_value("COMP_ROF") == "mosart"
@@ -144,6 +146,11 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     if config["COMP_OCN"] == "docn" and "aqua" in case.get_value("DOCN_MODE"):
         nmlgen.set_value("aqua_planet", value=".true.")
 
+    # make sure that variable add_gusts is only set to true if compset includes cam_dev
+    add_gusts = literal_to_python_value(nmlgen.get_value("add_gusts"), type_="logical")
+    if add_gusts:
+        expect("CAM%DEV" in case.get_value("COMPSET"),"ERROR: add_gusts can only be set if CAM%DEV in compset {}".format(case.get_value("COMPSET")))
+
     # --------------------------------
     # Overwrite: set component coupling frequencies
     # --------------------------------
@@ -658,6 +665,7 @@ def buildnml(case, caseroot, component):
     create_namelist_infile(case, user_nl_file, namelist_infile, infile_text)
     infile = [namelist_infile]
 
+
     # create the files nuopc.runconfig, nuopc.runseq, drv_in and drv_flds_in
     _create_drv_namelists(case, infile, confdir, nmlgen, files)
 

cime_config/config_component.xml

@@ -821,15 +821,6 @@
     different MPI ranks to different GPUs within the same compute node</desc>
   </entry>
 
-  <entry id="SMP_PRESENT">
-    <type>logical</type>
-    <valid_values>TRUE,FALSE</valid_values>
-    <default_value>FALSE</default_value>
-    <group>build_def</group>
-    <file>env_build.xml</file>
-    <desc>TRUE implies that at least one of the components is built threaded (DO NOT EDIT)</desc>
-  </entry>
-
   <entry id="ESMF_AWARE_THREADING">
     <type>logical</type>
     <valid_values>TRUE,FALSE</valid_values>
@@ -1035,23 +1026,6 @@
     this to work.</desc>
   </entry>
 
-  <entry id="ESMF_LOGFILE_KIND">
-    <type>char</type>
-    <valid_values>ESMF_LOGKIND_SINGLE,ESMF_LOGKIND_MULTI,ESMF_LOGKIND_NONE</valid_values>
-    <default_value>ESMF_LOGKIND_NONE</default_value>
-    <group>run_flags</group>
-    <file>env_run.xml</file>
-    <desc>
-      Determines what ESMF log files (if any) are generated when
-          USE_ESMF_LIB is TRUE.
-      ESMF_LOGKIND_SINGLE: Use a single log file, combining messages from
-          all of the PETs. Not supported on some platforms.
-      ESMF_LOGKIND_MULTI: Use multiple log files -- one per PET.
-      ESMF_LOGKIND_NONE: Do not issue messages to a log file.
-      By default, no ESMF log files are generated.
-    </desc>
-  </entry>
-
   <entry id="ESMF_VERBOSITY_LEVEL">
     <type>char</type>
     <valid_values>off,low,high,max</valid_values>

cime_config/namelist_definition_drv.xml

@@ -18,24 +18,6 @@
     </values>
   </entry>
 
-  <entry id="esmf_logging" modify_via_xml="ESMF_LOGFILE_KIND">
-    <type>char</type>
-    <category>cime_pes</category>
-    <group>PELAYOUT_attributes</group>
-    <desc>
-      Determines what ESMF log files (if any) are generated when
-          USE_ESMF_LIB is TRUE.
-      ESMF_LOGKIND_SINGLE: Use a single log file, combining messages from
-          all of the PETs. Not supported on some platforms.
-      ESMF_LOGKIND_MULTI: Use multiple log files — one per PET.
-      ESMF_LOGKIND_NONE: Do not issue messages to a log file.
-      By default, no ESMF log files are generated.
-    </desc>
-    <values>
-      <value>$ESMF_LOGFILE_KIND</value>
-    </values>
-  </entry>
-
   <entry id="pio_asyncio_ntasks" modify_via_xml="PIO_ASYNCIO_NTASKS">
     <type>integer</type>
     <category>pio</category>
@@ -964,6 +946,19 @@
     </values>
   </entry>
 
+  <entry id="add_gusts">
+    <type>logical</type>
+    <category>control</category>
+    <group>MED_attributes</group>
+    <desc>
+      add a wind gustiness factor
+    </desc>
+    <values>
+      <value CAMDEV="True">.true.</value>
+      <value CAMDEV="False">.false.</value>
+    </values>
+  </entry>
+
   <entry id="do_budgets" modify_via_xml="BUDGETS">
     <type>logical</type>
     <category>budget</category>

cime_config/runseq/runseq_TG.py

@@ -34,7 +34,7 @@ def gen_runseq(case, coupling_times):
         runseq.add_action ("MED med_phases_post_lnd"        , run_lnd)
         runseq.add_action ("MED med_phases_prep_glc"        , med_to_glc)
         runseq.add_action ("MED -> GLC :remapMethod=redist" , med_to_glc)
-        runseq.add_action ("GLC"                            , run_glc)
+        runseq.add_action ("GLC"                            , run_glc and med_to_glc)
         runseq.add_action ("GLC -> MED :remapMethod=redist" , run_glc)
         runseq.add_action ("MED med_phases_history_write"   , True)