Constituents

.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"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
       fail-fast: false
     steps:
     # Acquire github action routines:

Externals_CAM.cfg

@@ -1,8 +1,8 @@
 [ccpp-framework]
 local_path = ccpp_framework
 protocol = git
-repo_url = https://github.com/gold2718/ccpp-framework
-tag = CPF_0.2.032
+repo_url = https://github.com/peverwhee/ccpp-framework
+tag = CPF_0.2.039
 required = True
 
 [cosp2]

cime_config/cam_build_cache.py

@@ -100,6 +100,34 @@ def new_entry_from_xml(item):
     # end if
     return new_entry
 
+###############################################################################
+def clean_xml_text(item):
+###############################################################################
+    """Return a 'clean' (stripped) version of <item>.text or an empty
+       string if <item>.text is None or not a string-type variable
+
+       doctests
+
+       1. Test that the function works as expected when passed a string.
+       >>> test_xml = ET.Element("text")
+       >>> test_xml.text = " THIS IS A test "
+       >>> clean_xml_text(test_xml)
+       'THIS IS A test'
+
+       2. Verify that the function returns an empty string when not passed a string.
+       >>> test_xml = ET.Element("text")
+       >>> test_xml.text = 2
+       >>> clean_xml_text(test_xml)
+       ''
+
+    """
+    itext = item.text
+    iret = ""
+    if isinstance(itext, str):
+        iret = itext.strip()
+    # end if
+    return iret
+
 class FileStatus:
     """Class to hold full path and SHA hash of a file"""
 
@@ -219,13 +247,14 @@ def __init__(self, build_cache):
                         elif item.tag == 'config':
                             self.__config = item.text
                         elif item.tag == 'reg_gen_file':
-                            self.__reg_gen_files.append(item.text.strip())
+                            self.__reg_gen_files.append(clean_xml_text(item))
                         elif item.tag == 'ic_name_entry':
                             stdname = item.get('standard_name')
                             if stdname not in self.__ic_names:
                                 self.__ic_names[stdname] = []
                             # end if
-                            self.__ic_names[stdname].append(item.text.strip())
+                            itext = clean_xml_text(item)
+                            self.__ic_names[stdname].append(itext)
                         else:
                             emsg = "ERROR: Unknown registry tag, '{}'"
                             raise ValueError(emsg.format(item.tag))
@@ -248,16 +277,29 @@ def __init__(self, build_cache):
                             new_entry = new_entry_from_xml(item)
                             self.__xml_files[new_entry.key] = new_entry
                         elif item.tag == 'scheme_namelist_meta_file':
-                            self.__scheme_nl_metadata.append(item.text.strip())
+                            if isinstance(item.text, str):
+                                if item.text:
+                                    self.__scheme_nl_metadata.append(item.text.strip())
+                                # end if
+                            # end if
                         elif item.tag == 'scheme_namelist_groups':
-                            group_list = [x for x in
-                                          item.text.strip().split(' ') if x]
+                            group_list = []
+                            if isinstance(item.text, str):
+                                if item.text:
+                                    group_list = [x for x in
+                                                  item.text.strip().split(' ') if x]
+                                # end if
+                            # end if
                             self.__scheme_nl_groups = group_list
                         elif item.tag == 'preproc_defs':
-                            self.__preproc_defs = item.text.strip()
+                            self.__preproc_defs = clean_xml_text(item)
                         elif item.tag == 'kind_type':
-                            kname, ktype = item.text.strip().split('=')
-                            self.__kind_types[kname.strip()] = ktype.strip()
+                            if isinstance(item.text, str):
+                                if item.text:
+                                    kname, ktype = item.text.strip().split('=')
+                                    self.__kind_types[kname.strip()] = ktype.strip()
+                                # end if
+                            # end if
                         else:
                             emsg = "ERROR: Unknown CCPP tag, '{}'"
                             raise ValueError(emsg.format(item.tag))

cime_config/cam_config.py

@@ -250,7 +250,6 @@ def __init__(self, case, case_log):
         #Add the default host model namelists:
         self._add_xml_nml_file(cime_conf_path, "namelist_definition_cam.xml")
         self._add_xml_nml_file(data_nml_path, "namelist_definition_physconst.xml")
-        self._add_xml_nml_file(data_nml_path, "namelist_definition_air_comp.xml")
         self._add_xml_nml_file(data_nml_path, "namelist_definition_ref_pres.xml")
 
         #----------------------------------------------------

src/control/cam_comp.F90

@@ -10,25 +10,28 @@ module cam_comp
 !
 !-----------------------------------------------------------------------
 
-   use shr_kind_mod,    only: r8 => SHR_KIND_R8
-   use shr_kind_mod,    only: cl=>SHR_KIND_CL, cs=>SHR_KIND_CS
-   use shr_sys_mod,     only: shr_sys_flush
-
-   use spmd_utils,      only: masterproc, mpicom
-   use cam_control_mod, only: cam_ctrl_init, cam_ctrl_set_orbit, cam_ctrl_set_physics_type
-   use cam_control_mod, only: caseid, ctitle
-   use runtime_opts,    only: read_namelist
-   use runtime_obj,     only: cam_runtime_opts
-   use time_manager,    only: timemgr_init, get_step_size
-   use time_manager,    only: get_nstep, is_first_step, is_first_restart_step
-
-   use camsrfexch,      only: cam_out_t, cam_in_t
-   use physics_types,   only: phys_state, phys_tend
-   use dyn_comp,        only: dyn_import_t, dyn_export_t
-
-   use perf_mod,        only: t_barrierf, t_startf, t_stopf
-   use cam_logfile,     only: iulog
-   use cam_abortutils,  only: endrun
+   use shr_kind_mod,              only: r8 => SHR_KIND_R8
+   use shr_kind_mod,              only: cl=>SHR_KIND_CL, cs=>SHR_KIND_CS, cx=>SHR_KIND_CX
+   use shr_sys_mod,               only: shr_sys_flush
+
+   use spmd_utils,                only: masterproc, mpicom
+   use cam_control_mod,           only: cam_ctrl_init, cam_ctrl_set_orbit
+   use cam_control_mod,           only: cam_ctrl_set_physics_type
+   use cam_control_mod,           only: caseid, ctitle
+   use runtime_opts,              only: read_namelist
+   use runtime_obj,               only: cam_runtime_opts
+   use time_manager,              only: timemgr_init, get_step_size
+   use time_manager,              only: get_nstep
+   use time_manager,              only: is_first_step, is_first_restart_step
+
+   use camsrfexch,                only: cam_out_t, cam_in_t
+   use physics_types,             only: phys_state, phys_tend
+   use dyn_comp,                  only: dyn_import_t, dyn_export_t
+
+   use perf_mod,                  only: t_barrierf, t_startf, t_stopf
+   use cam_logfile,               only: iulog
+   use cam_abortutils,            only: endrun
+   use ccpp_constituent_prop_mod, only: ccpp_constituent_properties_t
 
    implicit none
    private
@@ -47,6 +50,16 @@ 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)
+
+   ! Private interface (here to avoid circular dependency)
+   private :: cam_register_constituents
+
+
 !-----------------------------------------------------------------------
 CONTAINS
 !-----------------------------------------------------------------------
@@ -80,6 +93,9 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
 !      use history_defaults,     only: initialize_iop_history
       use stepon,               only: stepon_init
       use air_composition,      only: air_composition_init
+      use cam_ccpp_cap,         only: cam_ccpp_initialize_constituents
+      use physics_grid,         only: columns_on_task
+      use vert_coord,           only: pver
 
       ! Arguments
       character(len=cl), intent(in) :: caseid                ! case ID
@@ -122,6 +138,8 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
 
                                                 ! Local variables
       character(len=cs)        :: filein        ! Input namelist filename
+      integer                  :: errflg
+      character(len=cx)        :: errmsg
       !-----------------------------------------------------------------------
 
       call init_pio_subsystem()
@@ -153,12 +171,20 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
       ! Open initial or restart file, and topo file if specified.
       call cam_initfiles_open()
 
-      ! Initialize model grids and decompositions
-      call model_grid_init()
+      ! Initialize constituent information
+      !    This will set the total number of constituents and the
+      !    number of advected constituents.
+      call cam_register_constituents(cam_runtime_opts)
 
       ! Initialize composition-dependent constants:
       call air_composition_init()
 
+      ! Initialize model grids and decompositions
+      call model_grid_init()
+
+      ! Initialize constituent data
+      call cam_ccpp_initialize_constituents(columns_on_task, pver, errflg, errmsg)
+
       ! Initialize ghg surface values before default initial distributions
       ! are set in dyn_init
       !!XXgoldyXX: This needs to be converted to CCPP and the issue of
@@ -461,6 +487,60 @@ subroutine cam_final(cam_out, cam_in)
 
    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 runtime_obj,               only: runtime_options
+      use cam_constituents,          only: cam_constituents_init
+      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
+
+      ! Dummy arguments
+      type(runtime_options), intent(in) :: cam_runtime_opts
+      ! Local variables
+      integer                                        :: index
+      integer                                        :: num_advect
+      integer,                           allocatable :: ind_water_spec(:)
+      integer                                        :: errflg
+      character(len=cx)                              :: 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)%initialize(std_name="specific_humidity",      &
+           long_name="Specific humidity", units="kg kg-1",                    &
+           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
+      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., &
+           errcode=errflg, errmsg=errmsg)
+
+      if (errflg /= 0) then
+         call endrun(subname//trim(errmsg), file=__FILE__, line=__LINE__)
+      end if
+
+      ! Grab a pointer to the constituent array
+      const_props => cam_model_const_properties()
+
+      ! Finally, initialize the constituents module
+      call cam_constituents_init(const_props, num_advect)
+
+   end subroutine cam_register_constituents
+
 !-----------------------------------------------------------------------
 
 end module cam_comp

src/control/cam_logfile.F90

@@ -28,12 +28,15 @@ module cam_logfile
 !-----------------------------------------------------------------------
 ! Public data ----------------------------------------------------------
 !-----------------------------------------------------------------------
-   integer, public, protected :: iulog = 6
    integer, public, parameter :: DEBUGOUT_NONE    = 0
    integer, public, parameter :: DEBUGOUT_INFO    = 1
    integer, public, parameter :: DEBUGOUT_VERBOSE = 2
    integer, public, parameter :: DEBUGOUT_DEBUG   = 3
    integer, public, protected :: debug_output = DEBUGOUT_NONE
+   !> \section arg_table_cam_logfile  Argument Table
+   !! \htmlinclude cam_logfile.html
+   integer, public, protected :: iulog = 6
+   logical, public, protected :: log_output = .false.
 
 !-----------------------------------------------------------------------
 ! Private data ---------------------------------------------------------
@@ -68,9 +71,9 @@ subroutine cam_set_log_unit(unit_num)
    end subroutine cam_set_log_unit
 
    subroutine cam_logfile_readnl(nlfile)
-      use shr_nl_mod,   only: find_group_name => shr_nl_find_group_name
-      use spmd_utils,   only: mpicom, masterprocid, masterproc
-      use mpi,          only: mpi_integer
+      use mpi,        only: mpi_integer
+      use shr_nl_mod, only: find_group_name => shr_nl_find_group_name
+      use spmd_utils, only: mpicom, masterprocid, masterproc
 
       ! nlfile: filepath for file containing namelist input
       character(len=*), intent(in) :: nlfile
@@ -84,6 +87,10 @@ subroutine cam_logfile_readnl(nlfile)
       namelist /cam_logfile_nl/ debug_output
       !------------------------------------------------------------------------
 
+      ! Since cam_set_log_unit is called before spmd_init is called,
+      !    set log_output flag here
+      log_output = masterproc
+
       if (masterproc) then
          open(newunit=unitn, file=trim(nlfile), status='old')
          call find_group_name(unitn, 'cam_logfile_nl', status=ierr)

src/control/cam_logfile.meta

@@ -0,0 +1,19 @@
+[ccpp-table-properties]
+  name = cam_logfile
+  type = module
+
+[ccpp-arg-table]
+  name  = cam_logfile
+  type  = module
+[ iulog ]
+  standard_name = log_output_unit
+  units = 1
+  type = integer
+  dimensions = ()
+  protected = True
+[ log_output ]
+  standard_name = do_log_output
+  units = flag
+  type = logical
+  dimensions = ()
+  protected = True

src/control/camsrfexch.F90

@@ -6,7 +6,6 @@ module camsrfexch
    !-----------------------------------------------------------------------
 
    use shr_kind_mod,    only: r8 => shr_kind_r8, r4 => shr_kind_r4
-   use constituents,    only: pcnst
    use shr_infnan_mod,  only: posinf => shr_infnan_posinf, assignment(=)
    use cam_abortutils,  only: endrun
    use string_utils,    only: to_str
@@ -155,7 +154,6 @@ subroutine cam_export(state, cam_out)
       use physics_types,    only: physics_state
       use vert_coord,       only: pver
       use physconst,        only: rair, mwdry, mwco2, gravit
-      use constituents,     only: pcnst
 
       ! Input arguments
       type(physics_state), intent(in)    :: state