Chemistry stub modules for MUSICA MICM

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 )
@@ -84,7 +95,7 @@ clean:
 	$(RM) $@ $*.mod
 ifeq "$(GEN_F90)" "true"
 	$(CPP) $(CPPFLAGS) $(PHYSICS) $(CPPINCLUDES) -I./inc $< > $*.f90
-	$(FC) $(FFLAGS) -c $*.f90 $(FCINCLUDES) -I../framework -I../operators -I./physics -I./dynamics -I./diagnostics -I./physics/physics_wrf -I./physics/physics_mmm -I./physics/physics_noaa/UGWP -I../external/esmf_time_f90
+	$(FC) $(FFLAGS) -c $*.f90 $(FCINCLUDES) -I../framework -I../operators -I./physics -I./dynamics -I./diagnostics -I./physics/physics_wrf -I./physics/physics_mmm -I./physics/physics_noaa/UGWP -I../external/esmf_time_f90 -I./chemistry
 else
-	$(FC) $(CPPFLAGS) $(PHYSICS) $(FFLAGS) -c $*.F $(CPPINCLUDES) $(FCINCLUDES) -I./inc -I../framework -I../operators -I./physics -I./dynamics -I./diagnostics -I./physics/physics_wrf -I./physics/physics_mmm -I./physics/physics_noaa/UGWP -I../external/esmf_time_f90
+	$(FC) $(CPPFLAGS) $(PHYSICS) $(FFLAGS) -c $*.F $(CPPINCLUDES) $(FCINCLUDES) -I./inc -I../framework -I../operators -I./physics -I./dynamics -I./diagnostics -I./physics/physics_wrf -I./physics/physics_mmm -I./physics/physics_noaa/UGWP -I../external/esmf_time_f90 -I./chemistry
 endif

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_atm_chemistry.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_atm_chemistry.F

@@ -0,0 +1,121 @@
+! Copyright (c) 2025 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 https://mpas-dev.github.io/license.html .
+!
+!-----------------------------------------------------------------------
+!  mpas_atm_chemistry
+!
+!> \brief Manages interactions with chemistry packages
+!> \author CheMPAS-A Developers
+!> \date   20 August 2025
+!> \details
+!>  This module manages the interactions with chemistry packages,
+!>  including initialization, time-stepping, and finalization.
+!>  It provides a framework for integrating various chemistry models
+!>  into the CheMPAS-A system.
+!
+!-------------------------------------------------------------------------
+module mpas_atm_chemistry
+
+    implicit none
+
+    private
+
+    public :: chemistry_init, chemistry_step, chemistry_finalize
+
+    contains
+
+    !------------------------------------------------------------------------
+    !  routine mpas_atm_chemistry_init
+    !
+    !> \brief Initializes the chemistry packages
+    !> \author CheMPAS-A Developers
+    !> \date   20 August 2025
+    !> \details
+    !>  This routine initializes the chemistry packages, setting up
+    !>  necessary parameters and data structures for the simulation.
+    !------------------------------------------------------------------------
+    ! subroutine chemistry_init(configs, number_of_grid_cells)
+    subroutine chemistry_init(number_of_grid_cells)
+
+#ifdef MPAS_USE_MUSICA
+        use mpas_musica, only: musica_init
+#endif
+        use mpas_log, only : mpas_log_write
+        use mpas_derived_types, only: mpas_pool_type
+        use mpas_kind_types, only: StrKIND
+        use mpas_pool_routines, only: mpas_pool_get_config 
+
+        ! type (mpas_pool_type),           intent(in)      :: configs
+        integer,                         intent(in)      :: number_of_grid_cells
+
+        integer                           :: error_code
+        character(len=:), allocatable     :: error_message
+        ! character(len=StrKIND), pointer   :: filepath
+        character(len=StrKIND)            :: filepath
+
+#ifdef MPAS_USE_MUSICA
+        ! call mpas_pool_get_config(configs, 'config_micm_file', filepath)
+        filepath = 'chapman.json'
+
+        call mpas_log_write('Initializing chemistry packages...')
+        call musica_init(filepath, number_of_grid_cells, error_code, error_message)
+
+        ! TODO check error_code and generate MPAS error log message
+#endif
+
+    end subroutine chemistry_init
+
+
+    !------------------------------------------------------------------------
+    !  routine mpas_atm_chemistry_step
+    !
+    !> \brief Steps the chemistry packages
+    !> \author CheMPAS-A Developers
+    !> \date   20 August 2025
+    !> \details
+    !>  This routine steps the chemistry packages, updating their state
+    !>  based on the current simulation time and conditions.
+    !------------------------------------------------------------------------
+    subroutine chemistry_step()
+
+#ifdef MPAS_USE_MUSICA
+        use mpas_musica, only: musica_step
+#endif
+        use mpas_log, only : mpas_log_write
+
+#ifdef MPAS_USE_MUSICA
+        call mpas_log_write('Stepping chemistry packages...')
+        ! call musica_step()
+#endif
+
+    end subroutine chemistry_step
+
+
+    !------------------------------------------------------------------------
+    !  routine mpas_atm_chemistry_finalize
+    !
+    !> \brief Finalizes the chemistry packages
+    !> \author CheMPAS-A Developers
+    !> \date   20 August 2025
+    !> \details
+    !>  This routine finalizes the chemistry packages, cleaning up
+    !>  any resources and data structures used during the simulation.
+    !------------------------------------------------------------------------
+    subroutine chemistry_finalize()
+
+#ifdef MPAS_USE_MUSICA
+        use mpas_musica, only: musica_finalize
+#endif
+        use mpas_log, only : mpas_log_write
+
+#ifdef MPAS_USE_MUSICA
+        call mpas_log_write('Finalizing chemistry packages...')
+        call musica_finalize()
+#endif
+
+    end subroutine chemistry_finalize
+
+end module mpas_atm_chemistry

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