Add a chemistry package structure

src/core_atmosphere/Makefile

@@ -2,29 +2,35 @@
 
 #
 # To build a dycore-only MPAS-Atmosphere model, comment-out or delete
-# the definition of PHYSICS, below
+# the definition of PHYSICS and CHEMISTRY, below
 #
-# If MPAS_CAM_DYCORE is found in CPPFLAGS, PHYSICS will become undefined automatically
+# If MPAS_CAM_DYCORE is found in CPPFLAGS, PHYSICS and CHEMISTRY will become undefined automatically
 #
 ifeq ($(findstring MPAS_CAM_DYCORE,$(CPPFLAGS)),)
     PHYSICS = -DDO_PHYSICS
+    CHEMISTRY = -DDO_CHEMISTRY
 endif
 
 ifdef PHYSICS
     PHYSCORE = physcore
     PHYS_OBJS = libphys/*.o
 endif
 
+ifdef CHEMISTRY
+    CHEMCORE = chemcore
+    CHEM_OBJS = libchem/*.o
+endif
+
 OBJS = mpas_atm_core.o \
        mpas_atm_core_interface.o \
        mpas_atm_dimensions.o \
        mpas_atm_threading.o \
        mpas_atm_halos.o
 
-all: $(PHYSCORE) dycore diagcore atmcore utilities
+all: $(PHYSCORE) $(CHEMCORE) dycore diagcore atmcore utilities
 
 core_reg:
-	$(CPP) $(CPPFLAGS) $(CPPINCLUDES) $(PHYSICS) Registry.xml > Registry_processed.xml
+	$(CPP) $(CPPFLAGS) $(CPPINCLUDES) $(PHYSICS) $(CHEMISTRY) Registry.xml > Registry_processed.xml
 
 core_input_gen:
 	if [ ! -e default_inputs ]; then  mkdir default_inputs; fi
@@ -47,17 +53,21 @@ physcore: mpas_atm_dimensions.o
 	( cd ../..; ln -sf ./src/core_atmosphere/physics/physics_wrf/files/*DATA* .)
 	( cd ../..; ln -sf ./src/core_atmosphere/physics/physics_noahmp/parameters/*TBL .)
 
-dycore: mpas_atm_dimensions.o $(PHYSCORE)
-	( cd dynamics; $(MAKE) all PHYSICS="$(PHYSICS)" )
+chemcore: mpas_atm_dimensions.o
+	( cd chemistry; $(MAKE) all )
+	( mkdir libchem; cd libchem; ar -x ../chemistry/libchem.a )
+
+dycore: mpas_atm_dimensions.o $(PHYSCORE) $(CHEMCORE)
+	( cd dynamics; $(MAKE) all PHYSICS="$(PHYSICS)"; $(MAKE) all CHEMISTRY="$(CHEMISTRY)" )
 
-diagcore: $(PHYSCORE) dycore
-	( cd diagnostics; $(MAKE) all PHYSICS="$(PHYSICS)" )
+diagcore: $(PHYSCORE) $(CHEMCORE) dycore
+	( cd diagnostics; $(MAKE) all PHYSICS="$(PHYSICS)"; $(MAKE) all CHEMISTRY="$(CHEMISTRY)" )
 
-utilities: $(PHYSCORE)
-	( cd utils; $(MAKE) all PHYSICS="$(PHYSICS)" )
+utilities: $(PHYSCORE) $(CHEMCORE)
+	( cd utils; $(MAKE) all PHYSICS="$(PHYSICS)"; $(MAKE) all CHEMISTRY="$(CHEMISTRY)" )
 
-atmcore: $(PHYSCORE) dycore diagcore $(OBJS)
-	ar -ru libdycore.a $(OBJS) dynamics/*.o $(PHYS_OBJS) diagnostics/*.o
+atmcore: $(PHYSCORE) $(CHEMCORE) dycore diagcore $(OBJS)
+	ar -ru libdycore.a $(OBJS) dynamics/*.o $(PHYS_OBJS) $(CHEM_OBJS) diagnostics/*.o
 
 mpas_atm_core_interface.o: mpas_atm_core.o
 
@@ -67,6 +77,7 @@ mpas_atm_dimensions.o:
 
 clean:
 	( cd physics; $(MAKE) clean )
+	( cd chemistry; $(MAKE) clean )
 	( cd dynamics; $(MAKE) clean )
 	( cd diagnostics; $(MAKE) clean )
 	( cd utils; $(MAKE) clean )

src/core_atmosphere/Registry.xml

@@ -1672,7 +1672,18 @@
 
                         <var name="nwfa" array_group="number" units="nb kg^{-1}"
                              description="Water-friendly aerosol number concentration"
-                             packages="mp_thompson_aers_in"/>
+				packages="mp_thompson_aers_in"/>
+
+		<!-- rkumar_chem_start -->
+			<var name="o3" array_group="chem" units="ppmv"
+			     description="ozone mixing ratio"/>
+
+			<var name="no" array_group="chem" units="ppmv"
+			     description="NO mixing ratio"/>
+
+			<var name="no2" array_group="chem" units="ppmv"
+			     description="NO2 mixing ratio"/>
+		<!-- rkumar_chem_end -->
                 </var_array>
 #endif
 
@@ -2023,7 +2034,18 @@
 
                         <var name="tend_nwfa" name_in_code="nwfa" array_group="number" units="nb m^{-3} s^{-1}"
                              description="Tendency of water-friendly aerosol number concentration multiplied by dry air density divided by d(zeta)/dz"
-                             packages="mp_thompson_aers_in"/>
+			     packages="mp_thompson_aers_in"/>
+
+		<!-- rkumar_chem_start -->
+                        <var name="tend_o3" name_in_code="o3" array_group="chem" units="ppmv s^{-1}"
+				description="Tendency of o3 mixing ratios"/>
+
+                        <var name="tend_no" name_in_code="no" array_group="chem" units="ppmv s^{-1}"
+				description="Tendency of no mixing ratios"/>
+
+                        <var name="tend_no2" name_in_code="no2" array_group="chem" units="ppmv s^{-1}"
+				description="Tendency of no2 mixing ratios"/>
+		<!-- rkumar_chem_end -->
                 </var_array>
 #endif
         </var_struct>

src/core_atmosphere/chemistry/Makefile

@@ -0,0 +1,41 @@
+.SUFFIXES: .F .o
+
+ifeq ($(CORE),atmosphere)
+COREDEF = -Dmpas
+endif
+
+all:
+	./../tools/manage_externals/checkout_externals --externals ./../Externals.cfg
+	$(MAKE) core_mpas_musica core_chemistry
+
+dummy:
+	echo "****** compiling chemistry ******"
+
+OBJS = \
+	mpas_atmchem_control.o
+
+core_mpas_musica:
+	(cd musica; $(MAKE) all COREDEF="$(COREDEF)")
+
+core_chemistry: core_mpas_musica
+	($(MAKE) chem_interface COREDEF="$(COREDEF)")
+	ar -ru libchem.a $(OBJS)
+	($(MAKE) -C ./musica mpas_musica_lib)
+
+chem_interface: $(OBJS)
+
+clean:
+	$(RM) *.o *.mod *.f90 libchem.a
+	( cd musica; $(MAKE) clean )
+	@# Certain systems with intel compilers generate *.i files
+	@# This removes them during the clean process
+	$(RM) *.i
+
+.F.o:
+	$(RM) $@ $*.mod
+ifeq "$(GEN_F90)" "true"
+	$(CPP) $(CPPFLAGS) $(COREDEF) $(HYDROSTATIC) $(CPPINCLUDES) $< > $*.f90
+	$(FC) $(FFLAGS) -c $*.f90 $(FCINCLUDES) -I./musica -I.. -I../../../framework -I../../../external/esmf_time_f90
+else
+	$(FC) $(CPPFLAGS) $(COREDEF) $(HYDROSTATIC) $(FFLAGS) -c $*.F $(CPPINCLUDES) $(FCINCLUDES) -I./musica -I.. -I../../../framework -I../../../external/esmf_time_f90
+endif

src/core_atmosphere/chemistry/mpas_atmchem_control.F

@@ -0,0 +1,37 @@
+! Copyright (c) 2025,  Los Alamos National Security, LLC (LANS)
+! and the University Corporation for Atmospheric Research (UCAR).
+!
+! Unless noted otherwise source code is licensed under the BSD license.
+! Additional copyright and license information can be found in the LICENSE file
+! distributed with this code, or at http://mpas-dev.github.com/license.html
+!
+!=================================================================================================================
+module mpas_atmchem_control
+
+
+  implicit none
+  private
+  public:: chemistry_setup_packages
+
+!MPAS chemistry package configuration routines.
+!ACOM Software Engineering Team 2025
+!
+! subroutines in mpas_atmchem_init:
+! ---------------------------------
+! chemistry_setup_packages : identifies available chemistry packages
+
+contains
+
+
+!=================================================================================================================
+ subroutine chemistry_setup_packages()
+!=================================================================================================================
+  use mpas_musica, only : log_musica_support
+
+  call log_musica_support()
+
+ end subroutine chemistry_setup_packages
+
+!=================================================================================================================
+end module mpas_atmchem_control
+!=================================================================================================================

src/core_atmosphere/chemistry/musica/Makefile

@@ -0,0 +1,30 @@
+.SUFFIXES: .F .o
+
+.PHONY: mpas_musica mpas_musica_lib
+
+all: dummy mpas_musica
+
+dummy:
+	echo "****** compiling mpas_musica ******"
+
+OBJS = \
+  mpas_musica.o
+
+mpas_musica: $(OBJS)
+
+mpas_musica_lib:
+	ar -ru ./../libchem.a $(OBJS)
+
+clean:
+	$(RM) *.f90 *.o *.mod
+	@# Certain systems with intel compilers generate *.i files
+	@# This removes them during the clean process
+	$(RM) *.i
+
+.F.o:
+ifeq "$(GEN_F90)" "true"
+	$(CPP) $(CPPFLAGS) $(COREDEF) $(CPPINCLUDES) $< > $*.f90
+	$(FC) $(FFLAGS) -c $*.f90 $(FCINCLUDES) -I.. -I../../../framework -I../../../external/esmf_time_f90
+else
+	$(FC) $(CPPFLAGS) $(COREDEF) $(FFLAGS) -c $*.F $(CPPINCLUDES) $(FCINCLUDES) -I.. -I../../../framework -I../../../external/esmf_time_f90
+endif

src/core_atmosphere/chemistry/musica/mpas_musica.F

@@ -0,0 +1,49 @@
+! Copyright (c) 2025 University Corporation for Atmospheric Research
+!
+! Unless noted otherwise, this software is licensed under the BSD license.
+! Additional copyright and license information can be found in the LICENSE file
+! distributed with this code, or at http://mpas-dev.github.com/license.html
+!
+!=================================================================================================================
+module mpas_musica
+#ifdef MPAS_USE_MUSICA
+  use musica_micm, only : get_micm_version
+  use musica_util, only : string_t
+#endif
+use mpas_log, only: mpas_log_write
+
+implicit none
+private
+public:: log_musica_support
+
+!The MUSICA library must also be compiled and linked to the MPAS executable, This is
+!typically done by first installing the MUSICA and then including the `MUSICA=true` option
+!when building the MPAS atmosphere model.
+!
+!CURRENTLY UNDER DEVELOPMENT
+!
+!ACOM Software Engineering Team 2025
+
+
+ contains
+
+
+!=================================================================================================================
+ subroutine log_musica_support()
+!=================================================================================================================
+#ifdef MPAS_USE_MUSICA
+
+!local variables
+  type(string_t) :: version_string
+
+  version_string = get_micm_version()
+  call mpas_log_write("MUSICA support is available. MICM version: "//version_string%value_)
+#else
+  call mpas_log_write("MUSICA support not available.")
+#endif
+ end subroutine log_musica_support
+
+!=================================================================================================================
+end module mpas_musica
+!=================================================================================================================
+

src/core_atmosphere/mpas_atm_core_interface.F

@@ -110,6 +110,10 @@ function atm_setup_packages(configs, streamInfo, packages, iocontext) result(ier
       use mpas_atmphys_packages
 #endif
 
+#ifdef DO_CHEMISTRY
+      use mpas_atmchem_control, only : chemistry_setup_packages
+#endif
+
       implicit none
 
       type (mpas_pool_type), intent(inout) :: configs
@@ -259,6 +263,10 @@ function atm_setup_packages(configs, streamInfo, packages, iocontext) result(ier
 
 #endif
 
+#ifdef DO_CHEMISTRY
+      call chemistry_setup_packages()
+#endif
+
    end function atm_setup_packages
 
 

src/core_init_atmosphere/Registry.xml

@@ -1171,6 +1171,15 @@
                         <var name="nwfa" array_group="number" units="nb kg^{-1}"
                              description="Gocart water-friendly aerosol number concentration"
                              packages="mp_thompson_aers_in"/>
+
+                        <var name="o3" array_group="chem" units="ppmv"
+                             description="ozone mixing ratio"/>
+
+                        <var name="no" array_group="chem" units="ppmv"
+                             description="no mixing ratio"/>
+
+                        <var name="no2" array_group="chem" units="ppmv"
+                             description="no2 mixing ratio"/>
                 </var_array>
 
                 <!-- Climatology for ocean mixed-layer depth -->

src/core_init_atmosphere/mpas_init_atm_cases.F

@@ -259,7 +259,11 @@ subroutine init_atm_setup_case(domain, stream_manager)
 
             call init_atm_case_gfs(block_ptr, mesh, nCells, nEdges, nVertLevels, fg, state, &
                                    diag, diag_physics, block_ptr % dimensions, block_ptr % configs)
-
+
+#ifdef DO_CHEMISTRY
+            call init_chem(mesh, state)
+#endif
+
             if (config_met_interp) then
                call init_atm_thompson_aerosols(block_ptr, mesh, block_ptr % configs, diag, state)
                call physics_initialize_real(mesh, fg, domain % dminfo, block_ptr % dimensions, block_ptr % configs)
@@ -7522,5 +7526,38 @@ function read_text_array(dminfo, filename, xarray) result(ierr)
 
    end function read_text_array
 
+   subroutine init_chem(mesh, state)
+
+      implicit none
+
+      type (mpas_pool_type), intent(in) :: mesh
+      type (mpas_pool_type), intent(inout) :: state
+
+      integer, pointer :: index_o3 
+      integer, pointer :: index_no 
+      integer, pointer :: index_no2 
+      integer, pointer :: nCells
+      integer, pointer :: nVertLevels 
+
+      integer :: k, iCell
+
+      real (kind=RKIND), dimension(:,:,:), pointer :: scalars
+
+      call mpas_log_write('====== Handling Chemistry initialization ======')
+
+      call mpas_pool_get_dimension(mesh, 'nCells', nCells)
+      call mpas_pool_get_dimension(mesh, 'nVertLevels', nVertLevels)
+
+      call mpas_pool_get_dimension(state, 'index_o3', index_o3)
+      call mpas_pool_get_dimension(state, 'index_no', index_no)
+      call mpas_pool_get_dimension(state, 'index_no2', index_no2)
+
+      call mpas_pool_get_array(state, 'scalars', scalars) 
+
+      scalars(index_o3,:,:) = 0.1
+      scalars(index_no,:,:) = 0.01
+      scalars(index_no2,:,:) = 0.03
+
+   end subroutine init_chem
 
 end module init_atm_cases