Use default value for initial chemical species mixing ratios

.gitmodules

@@ -20,7 +20,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = 2b66267fe263d9268effeaa1d47e3c03e6121d74
+	fxtag         = e92f76351e7f7703fb6d91cb5e76dcbbc6dcb3f2
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "rrtmgp-data"]

cime_config/atm_musica_config.py

@@ -8,4 +8,4 @@
 MUSICA_REPO_URL = "https://github.com/NCAR/musica.git"
 MUSICA_TAG = "25fff7ae42d146bf3f83ad5ac18b3caac8701ddd"
 CHEMISTRY_DATA_REPO_URL = "https://github.com/NCAR/cam-sima-chemistry-data.git"
-CHEMISTRY_DATA_TAG = "71ed143c54b0d5d6e3e70f3d05d413fddcf8d59e"
+CHEMISTRY_DATA_TAG = "1ea9d1b8b04980738894d30a864f9a000daf2e5c"

cime_config/buildlib

@@ -193,6 +193,15 @@ def _build_cam():
                     f'-I{os.path.join(musica_install_path, "include", "musica", "fortran")} '
                     '"'
                     )
+        else:
+            # If MUSICA scheme is not used, then copy over MUSICA
+            # source code file into a build directory, as it is needed
+            # by the temporary "musica_ccpp_dependencies.F90"
+            # CAM-SIMA file:
+            musica_species_src_path = os.path.join(atm_root, "src", "physics", "ncar_ccpp",
+                                                   "schemes", "musica", "util",
+                                                   "musica_ccpp_species.F90")
+            _copy2_as_needed(musica_species_src_path, phys_dirs[0])
 
         retcode, out, err = run_cmd(cmd)
         _LOGGER.info("Command %s:\n\nstdout:\n%s\n\nstderr:\n%s\n", cmd, out, err)
@@ -335,7 +344,7 @@ def _build_musica(clone_dest: str) -> str:
             cmake_build_type = "Debug"
         else:
             cmake_build_type = "Release"
-    
+
     command = [
         "cmake",
         f"-D CMAKE_INSTALL_PREFIX={install_dir}",

cime_config/namelist_definition_cam.xml

@@ -364,23 +364,6 @@
     </values>
   </entry>
 
-<!-- Host model chemistry settings -->
-
-  <entry id="musica_config">
-    <type>char*256</type>
-    <category>chemistry</category>
-    <group>chemistry_nl</group>
-    <desc>
-      Configuration option for the
-      MUSICA chemistry package.
-
-      Default: none
-    </desc>
-    <values>
-      <value>none</value>
-    </values>
-  </entry>
-
 <!-- Tropopause -->
   <entry id="tropopause_climo_file">
     <type>char*256</type>

src/control/cam_comp.F90

@@ -290,15 +290,18 @@ subroutine cam_timestep_init()
       !
       !-----------------------------------------------------------------------
 
-      use phys_comp,                only: phys_timestep_init
-      use physics_grid,             only: lat_rad, lon_rad
-      use orbital_data,             only: orbital_data_advance
-      use stepon,                   only: stepon_timestep_init
-      use cam_ccpp_cap,             only: cam_constituents_array
-      use ccpp_kinds,               only: kind_phys
-      use musica_ccpp_dependencies, only: set_initial_musica_concentrations
+      use phys_comp,                 only: phys_timestep_init
+      use physics_grid,              only: lat_rad, lon_rad
+      use orbital_data,              only: orbital_data_advance
+      use stepon,                    only: stepon_timestep_init
+      use cam_ccpp_cap,              only: cam_constituents_array
+      use cam_ccpp_cap,              only: cam_model_const_properties
+      use ccpp_constituent_prop_mod, only: ccpp_constituent_prop_ptr_t
+      use ccpp_kinds,                only: kind_phys
+      use musica_ccpp_dependencies,  only: set_initial_musica_concentrations
 
       real(kind_phys), pointer :: constituents_array(:,:,:)
+      type(ccpp_constituent_prop_ptr_t), pointer :: constituent_properties(:)
 
       ! Update current fractional calendar day. Needs to be updated at every timestep.
       calday = get_curr_calday()
@@ -331,7 +334,9 @@ subroutine cam_timestep_init()
       !----------------------------------------------------------
       if (is_first_timestep) then
          constituents_array => cam_constituents_array()
-         call set_initial_musica_concentrations(constituents_array)
+         constituent_properties => cam_model_const_properties()
+         call set_initial_musica_concentrations(constituents_array, &
+              constituent_properties)
       end if
 
       !

src/control/runtime_opts.F90

@@ -45,7 +45,6 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
       use inic_analytic_utils, only: analytic_ic_readnl
 
       use tropopause_climo_read, only: tropopause_climo_readnl
-      use musica_sima_namelist,  only: musica_ccpp_dependencies_readnl
 
 !      use tracers,             only: tracers_readnl
 !      use nudging,             only: nudging_readnl
@@ -103,7 +102,6 @@ subroutine read_namelist(nlfilename, single_column, scmlat, scmlon)
 !      call check_energy_readnl(nlfilename)
       call analytic_ic_readnl(nlfilename)
       call tropopause_climo_readnl(nlfilename)
-      call musica_ccpp_dependencies_readnl(nlfilename)
 !      call scam_readnl(nlfilename, single_column, scmlat, scmlon)
 !      call nudging_readnl(nlfilename)
 

src/physics/utils/musica_ccpp_dependencies.F90

@@ -47,8 +47,8 @@ module musica_ccpp_dependencies
   !> Indicator of whether MUSICA suite is being used
   logical :: is_musica_suite = .false.
 
-  !> Set of species for the current MUSICA configuration
-  type(species_t), allocatable :: musica_species(:)
+  !> Set of species for TUV-x
+  type(species_t), allocatable :: tuvx_species(:)
 
 !==============================================================================
 contains
@@ -84,20 +84,13 @@ subroutine initialize_musica_species_constituents(constituents_properties, &
     use ccpp_const_utils,          only: ccpp_const_get_idx
     use cam_logfile,               only: iulog
     use spmd_utils,                only: primary_process => masterproc
-    use musica_sima_namelist,      only: musica_config_str
 
     type(ccpp_constituent_prop_ptr_t), pointer :: constituents_properties(:)
     character(len=512),            intent(out) :: errmsg
     integer,                       intent(out) :: errcode
 
     ! local variables
-    character(len=*), parameter  :: chapman_config = 'chapman'
-    character(len=*), parameter  :: terminator_config = 'terminator'
-    logical                      :: is_chapman = .false.
-    logical                      :: is_terminator = .false.
-    integer                      :: num_micm_species = 0
-    integer                      :: num_tuvx_constituents = 1
-    integer                      :: num_tuvx_only_gas_species = 0
+    integer, parameter           :: num_tuvx_constituents = 4
     integer                      :: position
     integer                      :: constituent_index
     integer                      :: i_species
@@ -108,67 +101,28 @@ subroutine initialize_musica_species_constituents(constituents_properties, &
       return
     end if
 
-    ! Currently, we only support two types of MUSICA configurations: Chapman and Terminator,
-    ! until the file I/O object is implemented. If the configuration is neither of these,
-    ! an error will be thrown.
-    if (trim(musica_config_str) == "chapman") then
-      is_chapman = .true.
-      if (primary_process) then
-          write(iulog,*) "[MUSICA Info] Using the Chapman configuration with stubbed dependencies."
-      end if
-    else if (trim(musica_config_str) == "terminator") then
-      is_terminator = .true.
-      if (primary_process) then
-          write(iulog,*) "[MUSICA Info] Using the Terminator configuration with stubbed dependencies."
-      end if
-    else
-      errcode = 1
-      errmsg = "[MUSICA Error] MUSICA configuration is not found."
-      return
-    end if
-
-    if (is_chapman) then
-      num_micm_species = 5
-      num_tuvx_only_gas_species = 1
-    else if (is_terminator) then
-      num_micm_species = 2
-      num_tuvx_only_gas_species = 3
-    end if
-
-    allocate (musica_species(num_micm_species + num_tuvx_constituents + num_tuvx_only_gas_species), &
-      stat=errcode, errmsg=errmsg)
+    allocate (tuvx_species(num_tuvx_constituents), stat=errcode, errmsg=errmsg)
     if (errcode /= 0) return
 
-    musica_species(1) = species_t(&
+    tuvx_species(1) = species_t(&
         "cloud_liquid_water_mixing_ratio_wrt_moist_air_and_condensed_water", 0.0000060_kind_phys)
-
-    if (is_chapman) then
-      musica_species(2) = species_t("O2", 0.22474_kind_phys)
-      musica_species(3) = species_t("O", 5.3509e-10_kind_phys)
-      musica_species(4) = species_t("O1D", 5.3509e-10_kind_phys)
-      musica_species(5) = species_t("O3", 0.00016_kind_phys)
-      musica_species(6) = species_t("N2", 0.74015_kind_phys)
-      musica_species(7) = species_t("air", 1.0_kind_phys)
-
-    else if (is_terminator) then
-      musica_species(2) = species_t("Cl", 1.0e-12_kind_phys)
-      musica_species(3) = species_t("Cl2", 1.0e-12_kind_phys)
-      musica_species(4) = species_t("air", 1.0_kind_phys)
-      musica_species(5) = species_t("O2", 0.21_kind_phys)
-      musica_species(6) = species_t("O3", 4.0e-6_kind_phys)
-    end if
-
-    do i_species = 1, num_micm_species + num_tuvx_constituents + num_tuvx_only_gas_species
-      call ccpp_const_get_idx(constituents_properties, trim(musica_species(i_species)%name), &
-                              musica_species(i_species)%constituent_index, errmsg, errcode)
+    tuvx_species(2) = species_t("air", 1.0_kind_phys)
+    tuvx_species(3) = species_t("O2", 0.21_kind_phys)
+    tuvx_species(4) = species_t("O3", 4.0e-6_kind_phys)
+
+    do i_species = 1, num_tuvx_constituents
+      call ccpp_const_get_idx(constituents_properties, trim(tuvx_species(i_species)%name), &
+                              tuvx_species(i_species)%constituent_index, errmsg, errcode)
       if (errcode /= 0) return
     end do
 
   end subroutine initialize_musica_species_constituents
 
-  subroutine set_initial_musica_concentrations(constituents_array)
+  subroutine set_initial_musica_concentrations(constituents_array, constituent_properties)
 
-    use cam_abortutils, only: endrun
+    use cam_abortutils,            only: endrun
+    use ccpp_constituent_prop_mod, only: ccpp_constituent_prop_ptr_t
+    use musica_ccpp_species,       only: micm_species_set
 
     !-----------------------------------------------------------------------
     !
@@ -177,22 +131,35 @@ subroutine set_initial_musica_concentrations(constituents_array)
     !-----------------------------------------------------------------------
 
     real(kind_phys), intent(inout) :: constituents_array(:,:,:)
+    type(ccpp_constituent_prop_ptr_t), pointer, intent(inout) :: constituent_properties(:)
 
     ! local variables
-    integer :: i_species
+    integer            :: i_species, i_constituent
     character(len=512) :: errmsg
+    integer            :: errcode
+    real(kind_phys)    :: default_value
 
     ! Don't do anything if MUSICA suite is not being used
     if (.not. is_musica_suite) return
 
-    if (.not. allocated(musica_species)) then
+    if (.not. allocated(tuvx_species)) then
       errmsg = "[MUSICA Error] MUSICA species are not initialized."
       call endrun(errmsg, file=__FILE__, line=__LINE__)
     end if
 
-    do i_species = 1, size(musica_species)
-      constituents_array(:,:,musica_species(i_species)%constituent_index) = &
-        musica_species(i_species)%initial_mixing_ratio
+    do i_species = 1, size(tuvx_species)
+      constituents_array(:,:,tuvx_species(i_species)%constituent_index) = &
+        tuvx_species(i_species)%initial_mixing_ratio
+    end do
+
+    do i_species = 1, size(micm_species_set)
+      i_constituent = micm_species_set(i_species)%index_constituent_props
+      call constituent_properties(i_constituent)%default_value( &
+            default_value, errcode, errmsg)
+      if (errcode /= 0) then
+        call endrun(errmsg, file=__FILE__, line=__LINE__)
+      end if
+      constituents_array(:,:,i_constituent) = default_value
     end do
 
   end subroutine set_initial_musica_concentrations
@@ -205,7 +172,6 @@ subroutine musica_ccpp_dependencies_init( &
     use cam_logfile,               only: iulog
     use spmd_utils,                only: primary_process => masterproc
     use ccpp_constituent_prop_mod, only: ccpp_constituent_prop_ptr_t
-    use musica_sima_namelist,      only: musica_config_str
 
     !-----------------------------------------------------------------------
     !
@@ -228,12 +194,6 @@ subroutine musica_ccpp_dependencies_init( &
     if (trim(phys_suite_name) /= "musica") return
     is_musica_suite = .true.
 
-    if (trim(musica_config_str) == "none") then
-      errmsg = "[MUSICA Error] MUSICA configuration is not found. Please set musica_config to 'chapman' or 'terminator'."
-      errcode = 1
-      call endrun(errmsg, file=__FILE__, line=__LINE__)
-    end if
-
     if (primary_process) then
         write(iulog,*) 'WARNING: Using placeholder data for MUSICA chemistry.'
     end if