Merge pull request #232 from nusbaume/updated_standard_names

Update CAM-SIMA to run Kessler and Held-Suarez bit-for-bit with CAM
ESCOMP · Nov 8, 2023 · 7d299b6 · 7d299b6
2 parents ef838aa + 59fca03
commit 7d299b6
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diff --git a/.github/workflows/python_unit_tests.yml b/.github/workflows/python_unit_tests.yml
@@ -21,7 +21,7 @@ jobs:
     strategy:
       matrix:
         #All of these python versions will be used to run tests:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
       fail-fast: false
     steps:
     # Acquire github action routines:

diff --git a/Externals.cfg b/Externals.cfg
@@ -64,7 +64,7 @@ local_path = libraries/parallelio
 required = True
 
 [cime]
-tag = cime6.0.156
+tag = cime6.0.175
 protocol = git
 repo_url = https://github.com/ESMCI/cime
 local_path = cime

diff --git a/Externals_CAM.cfg b/Externals_CAM.cfg
@@ -2,36 +2,15 @@
 local_path = ccpp_framework
 protocol = git
 repo_url = https://github.com/peverwhee/ccpp-framework
-tag = CPF_0.2.045
+tag = CPF_0.2.050
 required = True
 
-[cosp2]
-local_path = src/physics/cosp2/src
-protocol = svn
-repo_url = https://github.com/CFMIP/COSPv2.0/tags/
-tag = v2.0.3cesm/src
-required = False
-
-[clubb]
-local_path = src/physics/clubb
-protocol = svn
-repo_url = https://svn-ccsm-models.cgd.ucar.edu/clubb_core/vendor_tags/
-tag = clubb_ncar_backwards_compat_20181205_c20190528
-required = False
-
 [ncar-physics]
 local_path = src/physics/ncar_ccpp
 protocol = git
-repo_url = https://github.com/NCAR/atmospheric_physics
-tag = atmos_phys0_00_020
+repo_url = https://github.com/ESCOMP/atmospheric_physics
+tag = atmos_phys0_01_000
 required = True
 
-[silhs]
-local_path = src/physics/silhs
-protocol = svn
-repo_url = https://svn-ccsm-models.cgd.ucar.edu/silhs/vendor_tags/
-tag = silhs_ncar_backwards_compat_20181205
-required = False
-
 [externals_description]
 schema_version = 1.0.0
diff --git a/cime_config/cam_autogen.py b/cime_config/cam_autogen.py
@@ -437,8 +437,8 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
         os.makedirs(physics_blddir)
     # End if
     # Collect all source directories
-    source_search = [source_mods_dir,
-                     os.path.join(atm_root, "src", "physics", "ncar_ccpp")]
+    atm_phys_src_dir = os.path.join(atm_root, "src", "physics", "ncar_ccpp")
+    source_search = [source_mods_dir, atm_phys_src_dir]
     # Find all metadata files, organize by scheme name
     all_scheme_files = _find_metadata_files(source_search, find_scheme_names)
 
@@ -449,8 +449,8 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
     for sdf in phys_suites_str.split(';'):
         sdf_path = _find_file(f"suite_{sdf}.xml", source_search)
         if not sdf_path:
-            emsg = "ERROR: Unable to find SDF for suite '{}'"
-            raise CamAutoGenError(emsg.format(sdf))
+            emsg = f"ERROR: Unable to find SDF for suite '{sdf}'"
+            raise CamAutoGenError(emsg)
         # End if
         sdfs.append(sdf_path)
         # Given an SDF, find all the schemes it calls
@@ -581,6 +581,30 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
         capgen_db = None
     # end if
 
+    # Several SIMA dycores need some of the physics schemes
+    # located in the "utilities" CCPP physics directory,
+    # even if the actual physics suites don't need them.
+    # So go-ahead and copy all of the source code from
+    # there to the bld directory:
+    if do_gen_ccpp:
+        # Set CCPP physics "utilities" path
+        atm_phys_util_dir = os.path.join(atm_phys_src_dir, "utilities")
+
+        # Check that directory exists
+        if not os.path.isdir(atm_phys_util_dir):
+            #CAM-SIMA will likely not run without this, so raise an error
+            emsg = "ERROR: Unable to find CCPP physics utilities directory:\n"
+            emsg += f" {atm_phys_util_dir}\n Have you run 'checkout_externals'?"
+            raise CamAutoGenError(emsg)
+        # end if
+
+        # Copy all utility source files to the build directory
+        atm_phys_util_files = glob.glob(os.path.join(atm_phys_util_dir, "*.F90"))
+        for util_file in atm_phys_util_files:
+            shutil.copy(util_file, physics_blddir)
+        # end for
+    # end if
+
     if do_gen_ccpp or do_gen_nl:
         # save build details in the build cache
         build_cache.update_ccpp(sdfs, scheme_files, host_files, xml_files,

diff --git a/cime_config/cam_config.py b/cime_config/cam_config.py
@@ -165,10 +165,9 @@ def __init__(self, case, case_log):
         and associated dictionary.
         """
 
-        # Check if using python 3.7 or later.  If not,
-        # then end build here:
-        if sys.version_info[0] < 3 or (sys.version_info[0] == 3 and sys.version_info[1] < 7):
-            emsg = "CAM requires python 3.7 or later, currently using python version"
+        # Check if using python 3.8 or later. If not, then end build here:
+        if sys.version_info[0] < 3 or (sys.version_info[0] == 3 and sys.version_info[1] < 8):
+            emsg = "SIMA requires python 3.8 or later, currently using python version"
             emsg += f" {sys.version_info[0]}.{sys.version_info[1]}"
             raise SystemError(emsg)
         #End if

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -165,7 +165,7 @@
       <value compset="_CAM%HS94">-phys held_suarez</value>
       <value compset="_CAM%KESSLER">-phys kessler -chem terminator -analytic_ic</value> -->
       <value compset="_CAM%KESSLER">--physics-suites kessler --analytic_ic</value>
-      <value compset="_CAM%FHS94">--physics-suites held_suarez_1994 --analytic_ic</value>
+      <value compset="_CAM%HS94">--physics-suites held_suarez_1994 --analytic_ic</value>
       <value compset="_CAM%PHYSTEST">--dyn none --physics-suites adiabatic</value>
 
       <!-- Aquaplanet -->

diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
@@ -84,14 +84,6 @@
     <science_support grid="T42_T42"/>
   </compset>
 
-  <compset>
-    <alias>FHS94</alias>
-    <lname>2000_CAM%HS94_SLND_SICE_SOCN_SROF_SGLC_SWAV</lname>
-    <science_support grid="T42z30_T42_mg17"/>
-    <science_support grid="T85z30_T85_mg17"/>
-    <science_support grid="T85z60_T85_mg17"/>
-  </compset>
-
   <!-- CAM aquaplanet compsets -->
 
   <compset>
@@ -149,6 +141,11 @@
     <lname>2000_CAM%ADIAB_SLND_SICE_SOCN_SROF_SGLC_SWAV</lname>
   </compset>
 
+  <compset>
+    <alias>FHS94</alias>
+    <lname>2000_CAM%HS94_SLND_SICE_SOCN_SROF_SGLC_SWAV</lname>
+  </compset>
+
   <!-- CAM Dycore test compsets -->
   <compset>
     <alias>FHIST_DARTC6</alias>
@@ -267,7 +264,7 @@
   </compset>
 
   <!-- Untested simple model compsets -->
-  
+
 
   <!-- ****************************** -->
   <!-- WACCM science supported compsets -->
@@ -540,7 +537,7 @@
  <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9x1.25_r%r05_g%gland4_w%null_m%gx1v7"	compset="2000_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV"	 >hybrid</value> -->
  <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9_1.25_r%r05_m%gx1v6"   compset="2000_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM1%NOEVOLVE_SWAV">hybrid</value> -->
  <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9_1.25_r%r05_m%gx1v6"   compset="2000_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV">hybrid</value> -->
-          
+
  <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9_1.25_r%r05_m%gx1v7"   compset="2000_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM1%NOEVOLVE_SWAV">hybrid</value> -->
  <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9_1.25_r%r05_m%gx1v7"   compset="2000_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV">hybrid</value> -->
  <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9x1.25_r%r05_g%gland4_w%null_m%gx1v7" compset="HIST_CAM60%WC.*_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV">hybrid</value> -->
@@ -554,7 +551,7 @@
 <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9x1.25_r%r05_g%gland4_w%null_m%gx1v7"	compset="HIST_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV"	 >b.e20.BHIST.f09_g17.20thC.297_01_v2</value> -->
 <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9_1.25_r%r05_m%gx1v6"   compset="2000_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM1%NOEVOLVE_SWAV">b.e16.B1850_WW3.f09_g16.lang_redi_2hr_frz_chl.003</value> -->
 <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9_1.25_r%r05_m%gx1v6"   compset="2000_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV">b.e20.B1850.f09_g16.pi_control.all.123</value> -->
-    
+
 <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9_1.25_r%r05_m%gx1v7"   compset="2000_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM1%NOEVOLVE_SWAV">b.e16.B1850_WW3.f09_g16.lang_redi_2hr_frz_chl.003</value> -->
 <!--	<value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9_1.25_r%r05_m%gx1v7"   compset="2000_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV">b.e20.B1850.f09_g16.pi_control.all.123</value> -->
 <!--        <value grid="a%0.9x1.25_l%0.9x1.25_oi%0.9x1.25_r%r05_g%gland4_w%null_m%gx1v7" compset="HIST_CAM60%WC.*_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV">b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001</value> -->

diff --git a/src/control/cam_comp.F90 b/src/control/cam_comp.F90
@@ -50,11 +50,10 @@ module cam_comp
 
    logical  :: BFB_CAM_SCAM_IOP = .false.
 
-   ! Currently, the host (CAM) only adds water vapor (specific_humidity)
-   !    as a constituent.
-   ! Does this need to be a configurable variable?
-   integer, parameter :: num_host_advected = 1
-   type(ccpp_constituent_properties_t), target :: host_constituents(num_host_advected)
+   ! Currently, the host (CAM-SIMA) adds only water vapor (specific humidity)
+   ! as a constituent when not requested by the physics.  However, it is
+   ! unclear if this is actually necessary.
+   type(ccpp_constituent_properties_t), allocatable, target :: host_constituents(:)
 
    ! Private interface (here to avoid circular dependency)
    private :: cam_register_constituents
@@ -492,41 +491,86 @@ end subroutine cam_final
    subroutine cam_register_constituents(cam_runtime_opts)
       ! Call the CCPP interface to register all constituents for the
       ! physics suite being invoked during this run.
-      use cam_abortutils,            only: endrun
+      use cam_abortutils,            only: endrun, check_allocate
       use runtime_obj,               only: runtime_options
+      use phys_comp,                 only: phys_suite_name
       use cam_constituents,          only: cam_constituents_init
+      use cam_constituents,          only: const_set_qmin, const_get_index
+      use ccpp_kinds,                only: kind_phys
       use ccpp_constituent_prop_mod, only: ccpp_constituent_prop_ptr_t
       use cam_ccpp_cap,              only: cam_ccpp_register_constituents
       use cam_ccpp_cap,              only: cam_ccpp_number_constituents
       use cam_ccpp_cap,              only: cam_model_const_properties
-      use cam_ccpp_cap,              only: cam_const_get_index
+      use cam_ccpp_cap,              only: cam_ccpp_is_scheme_constituent
 
       ! Dummy arguments
       type(runtime_options), intent(in) :: cam_runtime_opts
       ! Local variables
-      integer                                        :: index
+      logical                                        :: is_constituent
       integer                                        :: num_advect
-      integer,                           allocatable :: ind_water_spec(:)
+      integer                                        :: const_idx
       integer                                        :: errflg
-      character(len=cx)                              :: errmsg
+      character(len=512)                             :: errmsg
       type(ccpp_constituent_prop_ptr_t), pointer     :: const_props(:)
       character(len=*), parameter :: subname = 'cam_register_constituents: '
 
-      ! Register the constituents to find out what needs advecting
-      call host_constituents(1)%instantiate(std_name="specific_humidity",      &
-           long_name="Specific humidity", units="kg kg-1",                    &
-           vertical_dim="vertical_layer_dimension", advected=.true.,          &
-           errcode=errflg, errmsg=errmsg)
+      ! Initalize error flag and message:
+      errflg = 0
+      errmsg = ''
+
+      ! Check if water vapor is already marked as a constituent by the
+      ! physics:
+      call cam_ccpp_is_scheme_constituent(                                              &
+           "water_vapor_mixing_ratio_wrt_moist_air_and_condensed_water",                &
+           is_constituent, errflg, errmsg)
+
       if (errflg /= 0) then
          call endrun(subname//trim(errmsg), file=__FILE__, line=__LINE__)
       end if
-      call cam_ccpp_register_constituents(cam_runtime_opts%suite_as_list(),      &
+
+      !If not requested by the physics, then add water vapor to the
+      !constituents object:
+      !-------------------------------------------
+      if (.not. is_constituent) then
+
+         ! Allocate host_constituents object:
+         allocate(host_constituents(1), stat=errflg)
+         call check_allocate(errflg, subname, 'host_constituents(1)',                   &
+                             file=__FILE__, line=__LINE__)
+
+         ! Register the constituents so they can be advected:
+         call host_constituents(1)%instantiate( &
+              std_name="water_vapor_mixing_ratio_wrt_moist_air_and_condensed_water",    &
+              long_name="water vapor mixing ratio w.r.t moist air and condensed_water", &
+              units="kg kg-1",                                                          &
+              default_value=0._kind_phys,                                               &
+              vertical_dim="vertical_layer_dimension",                                  &
+              advected=.true.,                                                          &
+           errcode=errflg, errmsg=errmsg)
+
+         if (errflg /= 0) then
+            call endrun(subname//trim(errmsg), file=__FILE__, line=__LINE__)
+         end if
+      else
+         ! Allocate zero-size object so nothing is added
+         ! to main constituents object:
+         allocate(host_constituents(0), stat=errflg)
+         call check_allocate(errflg, subname, 'host_constituents(0)',                   &
+                             file=__FILE__, line=__LINE__)
+      end if
+      !-------------------------------------------
+
+      !Combine host and physics constituents into a single
+      !constituents object:
+      call cam_ccpp_register_constituents(cam_runtime_opts%suite_as_list(),             &
            host_constituents, errcode=errflg, errmsg=errmsg)
 
       if (errflg /= 0) then
          call endrun(subname//trim(errmsg), file=__FILE__, line=__LINE__)
       end if
-      call cam_ccpp_number_constituents(num_advect, advected=.true., &
+
+      !Determine total number of advected constituents:
+      call cam_ccpp_number_constituents(num_advect, advected=.true.,                    &
            errcode=errflg, errmsg=errmsg)
 
       if (errflg /= 0) then
@@ -536,9 +580,25 @@ subroutine cam_register_constituents(cam_runtime_opts)
       ! Grab a pointer to the constituent array
       const_props => cam_model_const_properties()
 
-      ! Finally, initialize the constituents module
+      ! Initialize the constituents module
       call cam_constituents_init(const_props, num_advect)
 
+      ! Finally, for CAM moist physics, one will need to use a
+      ! non-zero minimum value for water vapor, so update that
+      ! value here:
+      !-------------------------------------------
+      if (phys_suite_name /= 'held_suarez_1994') then !Held-Suarez is "dry" physics
+
+         ! Get constituent index for water vapor:
+         call const_get_index("water_vapor_mixing_ratio_wrt_moist_air_and_condensed_water", &
+                              const_idx)
+
+         ! Set new minimum value:
+         call const_set_qmin(const_idx, 1.E-12_kind_phys)
+      end if
+      !-------------------------------------------
+
+
    end subroutine cam_register_constituents
 
 !-----------------------------------------------------------------------