Update CMEPS for wave slow loop coupling and provide hooks for S2SW coupling through CMEPS

.github/pull_request_template.md

@@ -6,16 +6,13 @@ Contributors other than yourself, if any:
 
 CMEPS Issues Fixed (include github issue #):
 
-Are changes expected to change answers?
- - [ ] bit for bit
- - [ ] different at roundoff level
- - [ ] more substantial
+Are changes expected to change answers? (specify if bfb, different at roundoff, more substantial) 
 
 Any User Interface Changes (namelist or namelist defaults changes)?
- - [ ] Yes
- - [ ] No
 
-Testing performed if application target is CESM:(either UFS-S2S or CESM testing is required):
+### Testing performed
+
+Testing performed if application target is CESM:
 - [ ] (recommended) CIME_DRIVER=nuopc scripts_regression_tests.py
    - machines:
    - details (e.g. failed tests):
@@ -39,16 +36,14 @@ Testing performed if application target is UFS-HAFS:
    - description:
    - details (e.g. failed tests):
 
-Hashes used for testing:
+### Hashes used for testing:
+
 - [ ] CESM:
   - repository to check out: https://github.com/ESCOMP/CESM.git
-  - branch:
-  - hash:
+  - branch/hash:
 - [ ] UFS-coupled, then umbrella repostiory to check out and associated hash:
   - repository to check out:
-  - branch:
-  - hash:
+  - branch/hash:
 - [ ] UFS-HAFS, then umbrella repostiory to check out and associated hash:
   - repository to check out:
-  - branch:
-  - hash:
+  - branch/hash:

cesm/nuopc_cap_share/shr_fire_emis_mod.F90

@@ -42,7 +42,6 @@ module shr_fire_emis_mod
      character(len=name_len)             :: name            ! emissions component name (in fire emissions input table)
      integer                             :: index
      real(r8), pointer                   :: emis_factors(:) ! function of plant-function-type (PFT)
-     real(r8)                            :: coeff           ! emissions component coeffecient
      real(r8)                            :: molec_weight    ! molecular weight of the fire emissions compound (g/mole)
      type(shr_fire_emis_comp_t), pointer :: next_emiscomp   ! points to next member in the linked list
   endtype shr_fire_emis_comp_t
@@ -55,6 +54,7 @@ module shr_fire_emis_mod
   type shr_fire_emis_mechcomp_t
      character(len=16)             :: name                  ! compound name
      type(shr_fire_emis_comp_ptr), pointer :: emis_comps(:) ! an array of pointers to fire emis components
+     real(r8), pointer             :: coeffs(:)             ! coeffecients to emissions components
      integer                       :: n_emis_comps          ! number of fire emis compounds that make up the emissions for this mechanis compound
   end type shr_fire_emis_mechcomp_t
 
@@ -96,7 +96,7 @@ subroutine shr_fire_emis_readnl( NLFileName, emis_nflds )
     !     corresponding chemical tracers.
     !
     !-------------------------------------------------------------------------
-    
+
     ! input/output variables
     character(len=*), intent(in)  :: NLFileName  ! name of namelist file
     integer         , intent(out) :: emis_nflds
@@ -125,12 +125,12 @@ subroutine shr_fire_emis_readnl( NLFileName, emis_nflds )
     ! If other processes have already initialized megan - then the info will just be re-initialized
 
     call ESMF_VMGetCurrent(vm, rc=rc)
-    if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return 
+    if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return
 
     call ESMF_VMGet(vm, localPet=localPet, mpiCommunicator=mpicom, rc=rc)
-    if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return 
+    if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return
 
-    ! Note the following still needs to be called on all processors since the mpi_bcast is a collective 
+    ! Note the following still needs to be called on all processors since the mpi_bcast is a collective
     ! call on all the pes of mpicom
     if (localPet==0) then
        inquire( file=trim(NLFileName), exist=exists)
@@ -205,9 +205,12 @@ subroutine shr_fire_emis_init( specifier )
        endif
        shr_fire_emis_mechcomps(i)%n_emis_comps = item%n_terms
        allocate(shr_fire_emis_mechcomps(i)%emis_comps(item%n_terms))
+       allocate(shr_fire_emis_mechcomps(i)%coeffs(item%n_terms))
+
+       shr_fire_emis_mechcomps(i)%coeffs(:) = item%coeffs(:)
 
        do j = 1,item%n_terms
-          shr_fire_emis_mechcomps(i)%emis_comps(j)%ptr => add_emis_comp( item%vars(j), item%coeffs(j) )
+          shr_fire_emis_mechcomps(i)%emis_comps(j)%ptr => add_emis_comp( item%vars(j) )
        enddo
        shr_fire_emis_mechcomps_n = shr_fire_emis_mechcomps_n+1
 
@@ -224,10 +227,9 @@ end subroutine shr_fire_emis_init
 
   !-------------------------------------------------------------------------
 
-  function add_emis_comp( name, coeff ) result(emis_comp)
+  function add_emis_comp( name ) result(emis_comp)
 
     character(len=*), intent(in) :: name
-    real(r8),         intent(in) :: coeff
     type(shr_fire_emis_comp_t), pointer :: emis_comp
 
     emis_comp => get_emis_comp_by_name(shr_fire_emis_linkedlist, name)
@@ -245,7 +247,6 @@ function add_emis_comp( name, coeff ) result(emis_comp)
     emis_comp%index = shr_fire_emis_comps_n+1
 
     emis_comp%name = trim(name)
-    emis_comp%coeff = coeff
     nullify(emis_comp%next_emiscomp)
 
     call add_emis_comp_to_list(emis_comp)

cime_config/buildexe

@@ -37,7 +37,6 @@ def _main_func():
         cime_model = case.get_value("MODEL")
         num_esp   = case.get_value("NUM_COMP_INST_ESP")
         ocn_model = case.get_value("COMP_OCN")
-        atm_model = case.get_value("COMP_ATM")
         gmake_args = get_standard_makefile_args(case)
         esmf_aware_threading = case.get_value("ESMF_AWARE_THREADING")
 
@@ -63,7 +62,7 @@ def _main_func():
     else:
         skip_mediator = False
 
-    if ocn_model == 'mom' or atm_model == "ufsatm":
+    if ocn_model == 'mom':
         gmake_args += "USE_FMS=TRUE"
 
     comp_classes = case.get_values("COMP_CLASSES")

cime_config/buildnml

@@ -223,21 +223,21 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     # End if pause is active
 
     #--------------------------------
-    # (1) Specify input data list file
+    # Specify input data list file
     #--------------------------------
     data_list_path = os.path.join(case.get_case_root(), "Buildconf", "cpl.input_data_list")
     if os.path.exists(data_list_path):
         os.remove(data_list_path)
 
     #--------------------------------
-    # (2) Write namelist file drv_in and initial input dataset list.
+    # Write namelist file drv_in and initial input dataset list.
     #--------------------------------
     namelist_file = os.path.join(confdir, "drv_in")
     drv_namelist_groups = ["papi_inparm", "pio_default_inparm", "prof_inparm", "debug_inparm"]
     nmlgen.write_output_file(namelist_file, data_list_path=data_list_path, groups=drv_namelist_groups)
 
     #--------------------------------
-    # (3) Write nuopc.runconfig file and add to input dataset list.
+    # Write nuopc.runconfig file and add to input dataset list.
     #--------------------------------
 
     # Determine valid components
@@ -291,7 +291,7 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
     nmlgen.write_nuopc_config_file(nuopc_config_file, data_list_path=data_list_path)
 
     #--------------------------------
-    # (3.1) Update nuopc.runconfig file if component needs it
+    # Update nuopc.runconfig file if component needs it
     #--------------------------------
 
     # Read nuopc.runconfig
@@ -330,12 +330,12 @@ def _create_drv_namelists(case, infile, confdir, nmlgen, files):
                         f.write(line)
 
     #--------------------------------
-    # (4) Write nuopc.runseq
+    # Write nuopc.runseq
     #--------------------------------
     _create_runseq(case, coupling_times, valid_comps)
 
     #--------------------------------
-    # (5) Write drv_flds_in
+    # Write drv_flds_in
     #--------------------------------
     # In thte following, all values come simply from the infiles - no default values need to be added
     # FIXME - do want to add the possibility that will use a user definition file for drv_flds_in
@@ -567,7 +567,6 @@ def buildnml(case, caseroot, component):
     files.set_value("COMP_ROOT_DIR_CPL", comp_root_dir_cpl)
 
     definition_file = [files.get_value("NAMELIST_DEFINITION_FILE", {"component": "cpl"})]
-    fd_dir = os.path.dirname(definition_file[0])
     user_definition = os.path.join(user_xml_dir, "namelist_definition_drv.xml")
     if os.path.isfile(user_definition):
         definition_file = [user_definition]
@@ -606,15 +605,12 @@ def buildnml(case, caseroot, component):
     for filename in glob.glob(os.path.join(confdir, "*modelio*")):
         shutil.copy(filename, rundir)
 
-    # copy fd_cesm.yaml to rundir
-    fd_dir = os.path.join(os.path.dirname(__file__),os.pardir,"mediator")
-    coupling_mode = case.get_value('COUPLING_MODE')
-    if coupling_mode == 'cesm':
-        filename = os.path.join(fd_dir,"fd_cesm.yaml")
-    elif 'nems' in coupling_mode or coupling_mode == 'hafs':
-        filename = os.path.join(fd_dir,"fd_nems.yaml")
+    # copy fd_cesm.yaml to rundir - look in user_xml_dir first
+    user_yaml_file = os.path.join(user_xml_dir, "fd_cesm.yaml")
+    if os.path.isfile(user_yaml_file):
+        filename = user_yaml_file
     else:
-        expect(False, "coupling mode currently only supports cesm")
+        filename = os.path.join(os.path.dirname(__file__), os.pardir, "mediator", "fd_cesm.yaml")
     shutil.copy(filename, os.path.join(rundir, "fd.yaml"))
 
 ###############################################################################

cime_config/config_component.xml

@@ -28,7 +28,7 @@
 
   <entry id="COUPLING_MODE">
     <type>char</type>
-    <valid_values>cesm,nems_orig,nems_orig_data,nems_frac,hafs</valid_values>
+    <valid_values>cesm</valid_values>
     <default_value>cesm</default_value>
     <group>run_coupling</group>
     <file>env_run.xml</file>
@@ -1685,6 +1685,20 @@
     $CIMEROOT/machines/config_machines.xml</desc>
   </entry>
 
+  <entry id="DIN_STAGING_ROOT">
+    <type>char</type>
+    <default_value>UNSET</default_value>
+    <group>run_din</group>
+    <file>env_run.xml</file>
+    <desc>
+      On some systems the filesystem of DIN_LOC_ROOT is not available on compute nodes and
+      data must be staged to a temporary location.  If this variable is defined it will
+      be used as the root directory of an inputdata staging area.
+      Default values for the target machine are in the
+      $CIMEROOT/machines/config_machines.xml
+    </desc>
+  </entry>
+
   <entry id="DOUT_S_ROOT">
     <type>char</type>
     <default_value>UNSET</default_value>