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Chemistry stub modules for MUSICA MICM #1360

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29 changes: 20 additions & 9 deletions src/core_atmosphere/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -47,7 +53,11 @@ 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)
chemcore:
( cd chemistry; $(MAKE) all CHEMISTRY="$(CHEMISTRY)" )
( mkdir libchem; cd libchem; ar -x ../chemistry/libchem.a )

dycore: mpas_atm_dimensions.o $(PHYSCORE) $(CHEMCORE)
( cd dynamics; $(MAKE) all PHYSICS="$(PHYSICS)" )

diagcore: $(PHYSCORE) dycore
Expand All @@ -57,7 +67,7 @@ utilities: $(PHYSCORE)
( cd utils; $(MAKE) all PHYSICS="$(PHYSICS)" )

atmcore: $(PHYSCORE) dycore diagcore $(OBJS)
ar -ru libdycore.a $(OBJS) dynamics/*.o $(PHYS_OBJS) diagnostics/*.o
ar -ru libdycore.a $(OBJS) dynamics/*.o $(PHYS_OBJS) $(CHEM_OBJS) diagnostics/*.o

mpas_atm_core_interface.o: mpas_atm_core.o

Expand All @@ -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 )
Expand All @@ -83,8 +94,8 @@ clean:
.F.o:
$(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
$(CPP) $(CPPFLAGS) $(PHYSICS) $(CHEMISTRY) $(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 -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) $(CHEMISTRY) $(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
47 changes: 47 additions & 0 deletions src/core_atmosphere/chemistry/Makefile
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@@ -0,0 +1,47 @@
.SUFFIXES: .F .o

all:
ifeq ($(MUSICA),true)
echo "****** building MUSICA ******"
$(MAKE) core_mpas_musica core_chemistry
else
echo "****** not building MUSICA ******"
$(MAKE) core_chemistry
endif

dummy:
echo "****** compiling chemistry ******"

OBJS = \
mpas_atm_chemistry.o

ifeq ($(MUSICA),true)
core_mpas_musica:
echo "****** building CORE MPAS MUSICA ******"
(cd musica; $(MAKE) all)
endif

core_chemistry: $(if $(filter true,$(MUSICA)),core_mpas_musica)
($(MAKE) chem_interface)
ar -ru libchem.a $(OBJS)
ifeq ($(MUSICA),true)
($(MAKE) -C ./musica mpas_musica_lib)
endif

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) $(CPPINCLUDES) $< > $*.f90
$(FC) $(FFLAGS) -c $*.f90 $(FCINCLUDES) -I./musica -I.. -I../../framework -I../../../external/esmf_time_f90
else
$(FC) $(CPPFLAGS) $(FFLAGS) -c $*.F $(CPPINCLUDES) $(FCINCLUDES) -I./musica -I.. -I../../framework -I../../../external/esmf_time_f90
endif
126 changes: 126 additions & 0 deletions src/core_atmosphere/chemistry/mpas_atm_chemistry.F
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@@ -0,0 +1,126 @@
! 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 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, dimensions)

#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, mpas_pool_get_dimension

type (mpas_pool_type), intent(in) :: configs
type (mpas_pool_type), intent(in) :: dimensions

#ifdef MPAS_USE_MUSICA
integer :: error_code
character(len=:), allocatable :: error_message
integer :: nVertLevels
integer, pointer :: nVertLevels_ptr
! MUSICA will get the MICM JSON config from a namelist
! hardcode filepath for now
character(len=StrKIND) :: filepath = 'chapman.json'
#endif

call mpas_log_write('Initializing chemistry packages...')

#ifdef MPAS_USE_MUSICA
call mpas_pool_get_dimension(dimensions, 'nVertLevels', nVertLevels_ptr)
nVertLevels = nVertLevels_ptr

call musica_init(filepath, nVertLevels, error_code, error_message)

! TODO check error_code and generate MPAS error log message
#endif

end subroutine chemistry_init


!------------------------------------------------------------------------
! routine 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 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
31 changes: 31 additions & 0 deletions src/core_atmosphere/chemistry/musica/Makefile
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.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

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