Integration of CCPP-ized TJ2016 implementation (#271)

Updates atmospheric_physics to the latest tag bringing in TJ2016
capability and additional changes needed in support of TJ2016.

URL: #271

Describe any changes made to build system: N/A

Describe any changes made to the namelist: N/A

List any changes to the defaults for the boundary datasets: N/A

Describe any substantial timing or memory changes: N/A

Code reviewed by: nusbaume, peverwhee

List all existing files that have been modified, old files eliminated,
new files added and describe the changes:

M       Externals_CAM.cfg
- Updating to latest CCPP Framework needed for build.
- Updating to latest atmospheric_physics needed to bring in TJ2016.

M       src/control/cam_comp.F90
- Removing CAM suite and dynamic_constituents to match new API.

M       src/data/physconst.meta
- Updating two standard names.

M       src/data/registry.xml
A       src/dynamics/utils/hycoef.meta
- Exposing
sum_of_sigma_pressure_hybrid_coordinate_a_coefficient_and_sigma_pressure_hybrid_coordinate_b_coefficient
(etamid) to physics schemes.

M       src/dynamics/utils/hycoef.F90
- Updating lev, ilev, hybi, hyai to be read in by their standard names
and updating PIO checks appropriately.

A       tools/generate_input_to_stdnames_update.py
- Adding new script to convert CSV file exported from standard names
spreadsheet into the inputnames_dictionary.xml

M       tools/inputnames_to_stdnames.py
- Updating script to be tphysac/tphysbc aware to avoid duplicate
standard names in snapshots.

M       tools/stdnames_to_inputnames_dictionary.xml
- Adding missing entry for standard_gravitational_acceleration.

M       cime_config/testdefs/testlist_cam.xml
D        cime_config/testdefs/testmods_dirs/cam/outfrq_held_suarez_izumi_nooutput/shell_commands
D        cime_config/testdefs/testmods_dirs/cam/outfrq_held_suarez_izumi_nooutput/user_nl_cam
D        cime_config/testdefs/testmods_dirs/cam/outfrq_kessler_izumi_nooutput/shell_commands
D        cime_config/testdefs/testmods_dirs/cam/outfrq_kessler_izumi_nooutput/user_nl_cam
A        cime_config/testdefs/testmods_dirs/cam/outfrq_tj2016_derecho_nooutput/shell_commands
A        cime_config/testdefs/testmods_dirs/cam/outfrq_tj2016_derecho_nooutput/user_nl_cam
- Adding derecho build test for tj2016, updating existing tests to build
using both compilers (gnu and intel) and removing izumi tests based on
discussion from 7/15/24 to simplify test setup process.

If there were any failures reported from running test_driver.sh on any
test platform, and check in with these failures has been OK'd by the
gatekeeper, then copy the lines from the td.*.status files for the failed tests to
the appropriate machine below.  All failed tests must be justified.

derecho/intel/aux_cam
derecho/gnu/aux_cam
- All tests pass.

Summarize any changes to answers, i.e.,
- what code configurations: N/A
- what platforms/compilers: N/A
- nature of change (roundoff; larger than roundoff but same climate; new
climate): N/A

.gitmodules

@@ -1,9 +1,9 @@
 [submodule "ccpp-framework"]
         path          = ccpp_framework
-        url           = https://github.com/peverwhee/ccpp-framework
-        fxtag         = CPF_0.2.056
+        url           = https://github.com/NCAR/ccpp-framework
+        fxtag         = 2024-07-11-dev
         fxrequired    = AlwaysRequired
-        fxDONOTUSEurl = https://github.com/peverwhee/ccpp-framework
+        fxDONOTUSEurl = https://github.com/NCAR/ccpp-framework
 [submodule "mpas"]
         path          = src/dynamics/mpas/dycore
         url           = https://github.com/MPAS-Dev/MPAS-Model.git
@@ -14,7 +14,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
         url           = https://github.com/ESCOMP/atmospheric_physics
-        fxtag         = atmos_phys0_02_006
+        fxtag         = atmos_phys0_03_000
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "ccs_config"]

cime_config/testdefs/testlist_cam.xml

@@ -10,61 +10,53 @@
   <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_kessler_derecho_nooutput/">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_sima"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:10:00</option>
-      <option name="comment" >Intel build test for Kessler physics</option>
-    </options>
-  </test>
-  <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_held_suarez_derecho_nooutput/">
-    <machines>
       <machine name="derecho" compiler="gnu" category="aux_sima"/>
     </machines>
     <options>
       <option name="wallclock">00:10:00</option>
-      <option name="comment" >GNU build test for Held-Suarez physics</option>
+      <option name="comment">Intel build test for Kessler physics</option>
     </options>
   </test>
-
-  <!-- Derecho dycore tests -->
-  <test compset="FKESSLER" grid="mpasa480_mpasa480" name="SMS_Ln2" testmods="cam/outfrq_kessler_mpas_derecho_nooutput/">
+  <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_held_suarez_derecho_nooutput/">
     <machines>
+      <machine name="derecho" compiler="intel" category="aux_sima"/>
       <machine name="derecho" compiler="gnu" category="aux_sima"/>
     </machines>
     <options>
       <option name="wallclock">00:10:00</option>
-      <option name="comment" >GNU build test for MPAS dycore (with Kessler physics)</option>
+      <option name="comment">GNU build test for Held-Suarez physics</option>
     </options>
   </test>
-  <test compset="FKESSLER" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_kessler_se_cslam_derecho_nooutput/">
+  <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_tj2016_derecho_nooutput/">
     <machines>
+      <machine name="derecho" compiler="intel" category="aux_sima"/>
       <machine name="derecho" compiler="gnu" category="aux_sima"/>
     </machines>
     <options>
       <option name="wallclock">00:10:00</option>
-      <option name="comment" >GNU build test for SE-CSLAM dycore (with Kessler physics)</option>
+      <option name="comment">GNU build test for Moist Held-Suarez physics</option>
     </options>
-  </test>
+  </tests>
 
-  <!-- Izumi physics tests -->
-  <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_kessler_izumi_nooutput/">
+  <!-- Derecho dycore tests -->
+  <test compset="FKESSLER" grid="mpasa480_mpasa480" name="SMS_Ln2" testmods="cam/outfrq_kessler_mpas_derecho_nooutput/">
     <machines>
-      <machine name="izumi" compiler="gnu" category="aux_sima"/>
+      <machine name="derecho" compiler="intel" category="aux_sima"/>
+      <machine name="derecho" compiler="gnu" category="aux_sima"/>
     </machines>
     <options>
       <option name="wallclock">00:10:00</option>
-      <option name="comment" >GNU build test for Kessler physics</option>
+      <option name="comment">GNU build test for MPAS dycore (with Kessler physics)</option>
     </options>
   </test>
-  <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_held_suarez_izumi_nooutput/">
+  <test compset="FKESSLER" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_kessler_se_cslam_derecho_nooutput/">
     <machines>
-      <machine name="izumi" compiler="gnu" category="aux_sima"/>
+      <machine name="derecho" compiler="intel" category="aux_sima"/>
+      <machine name="derecho" compiler="gnu" category="aux_sima"/>
     </machines>
     <options>
       <option name="wallclock">00:10:00</option>
-      <option name="comment" >GNU build test for Held-Suarez physics</option>
+      <option name="comment">GNU build test for SE-CSLAM dycore (with Kessler physics)</option>
     </options>
   </test>
-
-
 </testlist>

cime_config/testdefs/testmods_dirs/cam/outfrq_tj2016_derecho_nooutput/shell_commands

@@ -0,0 +1 @@
+ ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites tj2016"

cime_config/testdefs/testmods_dirs/cam/outfrq_tj2016_derecho_nooutput/user_nl_cam

@@ -0,0 +1,4 @@
+ncdata=/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots/cam_tj2016_precip_tend_ne3pg3mg37_derecho_gnu_before.nc
+ncdata_check=/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots/cam_tj2016_precip_tend_ne3pg3mg37_derecho_gnu_after.nc
+debug_output=0
+pver=30

src/control/cam_comp.F90

@@ -612,8 +612,8 @@ subroutine cam_register_constituents(cam_runtime_opts)
 
       !Combine host and physics constituents into a single
       !constituents object:
-      call cam_ccpp_register_constituents(cam_runtime_opts%suite_as_list(),             &
-           host_constituents, dynamic_constituents, errcode=errflg, errmsg=errmsg)
+      call cam_ccpp_register_constituents(             &
+           host_constituents, errcode=errflg, errmsg=errmsg)
 
       if (errflg /= 0) then
          call endrun(subname//trim(errmsg), file=__FILE__, line=__LINE__)

src/data/physconst.meta

@@ -201,7 +201,7 @@
   dimensions = ()
   protected = True
 [ gravit ]
-  standard_name = gravitational_acceleration
+  standard_name = standard_gravitational_acceleration
   units = m s-2
   type = real | kind = kind_phys
   dimensions = ()
@@ -268,7 +268,7 @@
   dimensions = ()
   protected = True
 [ epsilo ]
-  standard_name = ratio_of_h2o_to_dry_air_molecular_weights
+  standard_name = ratio_of_water_vapor_to_dry_air_molecular_weights
   units = 1
   type = real | kind = kind_phys
   dimensions = ()

src/data/registry.xml

@@ -14,6 +14,7 @@
   <metadata_file>$SRCROOT/src/data/cam_thermo.meta</metadata_file>
   <metadata_file>$SRCROOT/src/data/ref_pres.meta</metadata_file>
   <metadata_file>$SRCROOT/src/dynamics/utils/vert_coord.meta</metadata_file>
+  <metadata_file>$SRCROOT/src/dynamics/utils/hycoef.meta</metadata_file>
   <!-- Variables registered to physics_types -->
   <file name="physics_types" type="module">
     <use module="ccpp_kinds" reference="kind_phys"/>

src/dynamics/utils/hycoef.F90

@@ -1,6 +1,7 @@
 module hycoef
 
 use shr_kind_mod,     only: r8 => shr_kind_r8
+use ccpp_kinds,       only: kind_phys
 use spmd_utils,       only: masterproc
 use vert_coord,       only: pver, pverp
 use cam_logfile,      only: iulog
@@ -28,8 +29,6 @@ module hycoef
 real(r8), public, allocatable, target :: hybi(:)  ! ps component of hybrid coordinate - interfaces
 real(r8), public, allocatable, target :: hybm(:)  ! ps component of hybrid coordinate - midpoints
 
-real(r8), public, allocatable :: etamid(:)  ! hybrid coordinate - midpoints
-
 real(r8), public, allocatable :: hybd(:)    ! difference  in b (hybi) across layers
 real(r8), public, allocatable :: hypi(:)    ! reference pressures at interfaces
 real(r8), public, allocatable :: hypm(:)    ! reference pressures at midpoints
@@ -47,6 +46,10 @@ module hycoef
 type(var_desc_t) :: hyam_desc, hyai_desc, hybm_desc, hybi_desc, p0_desc
 public init_restart_hycoef, write_restart_hycoef
 
+!> \section arg_table_hycoef  Argument Table
+!! \htmlinclude hycoef.html
+real(kind_phys), allocatable, public :: etamid(:)  ! hybrid coordinate - midpoints
+
 !=======================================================================
 contains
 !=======================================================================
@@ -56,6 +59,7 @@ subroutine hycoef_init(file, psdry)
 !   use cam_history_support, only: add_hist_coord, add_vert_coord, formula_terms_t
    use physconst,    only: pref
    use string_utils, only: to_str
+   use phys_vars_init_check, only: mark_as_initialized
 
    !-----------------------------------------------------------------------
    !
@@ -326,6 +330,11 @@ subroutine hycoef_init(file, psdry)
       write(iulog,9830) pverp, hypi(pverp)
     end if
 
+    ! Mark etamid (input name) as initialized (by standard name sum_of_sigma_...)
+    call mark_as_initialized( &
+      'sum_of_sigma_pressure_hybrid_coordinate_a_coefficient_and_sigma_pressure_hybrid_coordinate_b_coefficient')
+
+
 9800 format( 1x, i3, 3p, 3(f10.4,10x) )
 9810 format( 1x, 3x, 3p, 3(10x,f10.4) )
 9820 format(1x,'reference pressures (Pa)')
@@ -394,42 +403,101 @@ subroutine hycoef_read(File)
    character(len=*), parameter :: routine = 'hycoef_read'
    !----------------------------------------------------------------------------
 
+   ! Set PIO to return error codes.
+   call pio_seterrorhandling(file, PIO_BCAST_ERROR, pio_errtype)
+
    ! PIO traps errors internally, no need to check ierr
 
    ierr = PIO_Inq_DimID(File, 'lev', lev_dimid)
+   if (ierr /= PIO_NOERR) then
+      ierr = PIO_Inq_DimID(File, 'reference_pressure_in_atmosphere_layer', lev_dimid)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': ERROR: unable to find lev dimension in ncdata or restart file.')
+      end if
+   end if
    ierr = PIO_Inq_dimlen(File, lev_dimid, flev)
+   if (ierr /= PIO_NOERR) then
+      call endrun(routine//': ERROR: Failed to inquire dimension length of flev in ncdata or restart file.')
+   end if
    if (pver /= flev) then
       write(iulog,*) routine//': ERROR: file lev does not match model. lev (file, model):',flev, pver
       call endrun(routine//': ERROR: file lev does not match model.')
    end if
 
    ierr = PIO_Inq_DimID(File, 'ilev', lev_dimid)
+   if (ierr /= PIO_NOERR) then
+      ierr = PIO_Inq_DimID(File, 'reference_pressure_in_atmosphere_layer_at_interfaces', lev_dimid)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': ERROR: unable to find ilev dimension in ncdata or restart file')
+      end if
+   end if
    ierr = PIO_Inq_dimlen(File, lev_dimid, filev)
+   if (ierr /= PIO_NOERR) then
+      call endrun(routine//': ERROR: Failed to inquire dimension length of filev in ncdata or restart file.')
+   end if
    if (pverp /= filev) then
       write(iulog,*) routine//':ERROR: file ilev does not match model ilev (file, model):',filev, pverp
       call endrun(routine//':ERROR: file ilev does not match model.')
    end if
 
    ierr = pio_inq_varid(File, 'hyai', hyai_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'sigma_pressure_hybrid_coordinate_a_coefficient_at_interfaces', hyai_desc)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': ERROR: unable to find hyai variable in ncdata or restart file')
+      end if
+   end if
+
    ierr = pio_inq_varid(File, 'hyam', hyam_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'sigma_pressure_hybrid_coordinate_a_coefficient', hyam_desc)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': ERROR: unable to find hyam variable in ncdata or restart file')
+      end if
+   end if
+
    ierr = pio_inq_varid(File, 'hybi', hybi_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'sigma_pressure_hybrid_coordinate_b_coefficient_at_interfaces', hybi_desc)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': ERROR: unable to find hybi variable in ncdata or restart file')
+      end if
+   end if
+
    ierr = pio_inq_varid(File, 'hybm', hybm_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'sigma_pressure_hybrid_coordinate_b_coefficient', hybm_desc)
+      if (ierr /= PIO_NOERR) then
+         call endrun(routine//': ERROR: unable to find hybm variable in ncdata or restart file')
+      end if
+   end if
 
    ierr = pio_get_var(File, hyai_desc, hyai)
+   if (ierr /= PIO_NOERR) then
+     call endrun(routine//': ERROR: Unable to get hyai variable in ncdata or restart file.')
+   end if
    ierr = pio_get_var(File, hybi_desc, hybi)
+   if (ierr /= PIO_NOERR) then
+     call endrun(routine//': ERROR: Unable to get hybi variable in ncdata or restart file.')
+   end if
    ierr = pio_get_var(File, hyam_desc, hyam)
+   if (ierr /= PIO_NOERR) then
+     call endrun(routine//': ERROR: Unable to get hyam variable in ncdata or restart file.')
+   end if
    ierr = pio_get_var(File, hybm_desc, hybm)
+   if (ierr /= PIO_NOERR) then
+     call endrun(routine//': ERROR: Unable to get hybm variable in ncdata or restart file.')
+   end if
 
    if (masterproc) then
       write(iulog,*) routine//': read hyai, hybi, hyam, hybm'
    end if
 
    ! Check whether file contains value for P0.  If it does then use it
-
-   ! Set PIO to return error codes.
-   call pio_seterrorhandling(file, PIO_BCAST_ERROR, pio_errtype)
-
    ierr = pio_inq_varid(file, 'P0', p0_desc)
+   if (ierr /= PIO_NOERR) then
+      ierr = pio_inq_varid(File, 'surface_reference_pressure', p0_desc)
+   end if
    if (ierr == PIO_NOERR) then
       ierr = pio_get_var(file, p0_desc, ps0)
       if (ierr /= PIO_NOERR) then

src/dynamics/utils/hycoef.meta

@@ -0,0 +1,13 @@
+[ccpp-table-properties]
+  name = hycoef
+  type = module
+[ccpp-arg-table]
+  name = hycoef
+  type = module
+
+[ etamid ]
+  standard_name = sum_of_sigma_pressure_hybrid_coordinate_a_coefficient_and_sigma_pressure_hybrid_coordinate_b_coefficient
+  type = real | kind = kind_phys
+  units = 1
+  dimensions = (vertical_layer_dimension)
+