Use default value for initial chemical species mixing ratios (#405)

Tag name (required for release branches):
Originator(s): Matt Dawson

Description (include the issue title, and the keyword ['closes',
'fixes', 'resolves'] followed by the issue number):
This PR updates to use a newer version of `atmospheric_physics` that
includes setting the `default_value` of constituent instances created
for chemical species based on data in the MICM species configuration
files. The updates to CAM-SIMA remove the hard-coded initial species
mixing ratios for Terminator and Chapman mechanisms and instead set the
initial mixing ratios for chemical species based on the `default_value`
of the corresponding constituent, which allows any mechanism to be run.
This is needed to demonstrate the run-time configurability of the
chemical system.

@nusbaume - I wasn't sure if the logic for setting default values for
constituents should be restricted to chemical species or not. If it
makes sense to set this value for any constituent, I can modify this PR,
but would need some guidance on where in the workflow to set the default
value to avoid overwriting conditions explicitly set in other parts of
the code.

Describe any changes made to build system:
updated commits for `atmospheric_physics` and `cam-sima-chemistry-data`
repos.

Describe any changes made to the namelist:
none

List any changes to the defaults for the input datasets (e.g. boundary
datasets):
none

List all files eliminated and why:
`musica_sima_namelist.F90` - no namelist parameters are needed for
musica now that CAM-SIMA is not restricted to Terminator and Chapman

List all files added and what they do:
none

List all existing files that have been modified, and describe the
changes:
(Helpful git command: `git diff --name-status
development...<your_branch_name>`)
| File | Description |

|-----------------------------------------------|-------------------------------------------------------------------------|
| src/physics/utils/musica_sima_namelist.F90 | Removed use of deleted
musica namelist module |
| src/physics/utils/musica_ccpp_dependencies.F90| Replaced hard-coded
initial mixing ratios for MICM species with constituent `default_value`
|
| src/control/runtime_opts.F90 | Removed call to
`musica_ccpp_dependencies_readnl` |
| src/control/cam_comp.F90 | Updated `set_initial_musica_concentrations`
call to include properties for accessing `default_value` |
| cime_config/atm_musica_config.py | Updated `CHEMISTRY_DATA_TAG` |
| .gitmodules | Updated `atmospheric_physics` submodule tag |
</details>



If there are new failures (compared to the
`test/existing-test-failures.txt` file),
have them OK'd by the gatekeeper, note them here, and add them to the
file.
If there are baseline differences, include the test and the reason for
the
diff. What is the nature of the change? Roundoff?
will add after tests are run

derecho/intel/aux_sima:

derecho/gnu/aux_sima:

If this changes climate describe any run(s) done to evaluate the new
climate in enough detail that it(they) could be reproduced:
this should only affect chemistry

CAM-SIMA date used for the baseline comparison tests if different than
latest:

---------

Co-authored-by: Jesse Nusbaumer <nusbaume@ucar.edu>

Author: mattldawson

.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/ncar_ccpp

@@ -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