Merge branch 'release-v8.4.0'

MPAS Version 8.4.0

This release of MPAS introduces new capabilities and improvements in the
MPAS-Atmosphere model and its supporting software infrastructure, and it is the
first release to provide the foundation for CheMPAS-A, a chemistry capability
for MPAS-Atmosphere. Notable changes are listed below.

MPAS-Atmosphere Initialization:

 * Fix an issue in snow initialization over areas covered by seaice. (PR #1438)

 * Introduce namelist control over the vertical coordinate configuration for
   real-data case initialization. Two new namelist options may now be specified
   in the &vertical_grid namelist group in the namelist.init_atmosphere file:

    - config_hybrid_coordinate (default: true)
      Whether to employ a hybrid vertical coordinate

    - config_hybrid_top_z (default: 30000 m)
      Height at which coordinate surfaces become constant height surfaces

   Additionally, the smoothing coefficient formula for the hybrid coordinate now
   uses the transition height instead of the model top height. (PR #1382)

 * Add computation of the edgeNormalVectors, cellTangentPlane, and
   localVerticalUnitVectors fields for MPAS-A initialization case 13 (CAM-MPAS
   3-d grid) to better support alternative initialization workflows for
   CAM-MPAS. (PR #1351)

MPAS-Atmosphere Dynamics:

 * Implement an initial Large-Eddy Simulation (LES) capability. Similar to WRF,
   it contains two subgrid turbulence models -- a diagnostic Turbulent Kinetic
   Energy (TKE) formulation based on a 3-d Smagorinsky formulation, and a
   1.5-order prognostic TKE formulation. These formulations generally follow
   the implementation in WRF (see the WRF Technical Note Version 4, sections
   4.2.3 and 4.2.4 for a description of the formulations). (PR #1404)

 * Generalize the epssm parameter, allowing level-dependent values to be
   specified through four new namelist options:

    - config_epssm_minimum (default value: 0.1)
    - config_epssm_maximum (default value: 0.5)
    - config_epssm_transition_bottom_z (default value: 30000.0)
    - config_epssm_transition_top_z (default value: 50000.0)

   The epssm parameter is an off-centering coefficient for the vertically
   semi-implicit acoustic / gravity-wave integration, and it was previously
   specified as a single, constant value using the config_epssm namelist option.
   (PR #1381)

 * Add the capability to turn off microphysics tendencies above a specified
   height with a new namelist option, config_microphysics_top, in the &physics
   namelist group. Ignoring tendencies from the microphysics at upper levels has
   been found to alleviate some instabilities in deep-domain (i.e., model tops
   above the stratopause) MPAS-Atmosphere simulations. (PR #1380)

 * Optimize OpenACC data movement throughout the MPAS-A dycore, so that the
   majority of fields are transferred to the device at the start of a dynamics
   step and from the device at the end of a dynamics step. (PR #1315)

 * Remove the scaling of the gravity-wave absorbing layer coefficient (dss) by
   the local mesh size. Previously, the absorbing layer coefficient was scaled
   by dx/dx_fine, and for large values of dx/dx_fine, instabilities have been
   encountered associated with this scaling of the absorbing layer coefficient.
   (PR #1379)

MPAS-Atmosphere Physics:

 * Correct an issue with high q2 values over urban cells in Noah-MP. (PR #1383)

 * Fix crashes when using the CAM SW radiation scheme. (PR #1391)

 * Fix an indexing typo in mpas_atmphys_interface.F, where evapprod(k,k) was
   used instead of evapprod(k,i). The fix corrects diagnostic output, but should
   not affect the model state or simulation results. (PR #1396)

 * Correct the units designations of the gravity wave drag diagnostics variables
   dusfcg, dvsfcg, dtaux3d and dtauy3d in the atmosphere core's Registry.xml
   file. (PR #1378)

MPAS-Atmosphere Misc.:

 * Remove PV diagnostic fields from the default "output" stream for
   MPAS-Atmosphere, reducing the size of the default "history" netCDF files by
   ~20%. (PR #1428)

 * Modify the MPAS-Atmosphere CMake build system to use manage_externals to
   obtain specific tags from the https://github.com/NCAR/MMM-physics.git and
   https://github.com/NOAA-GSL/UGWP.git repositories, rather than simply
   obtaining the HEAD of the default branch. This modification corrects build
   failures when using CMake. (PR #1421)

CheMPAS-A:

 * Enable linking with the MUSICA-Fortran library to support development of
   chemistry capabilities based on MICM and TUV-x. (PR #1309)

 * Add a new namelist group, &musica, with a single option, config_micm_file, to
   control the MICM configuration in MPAS-Atmosphere. The new namelist group is
   only included in the namelist.atmosphere file (and therefore, only
   recognized) when MPAS is compiled with support for the MUSICA library.
   (PR #1376)

 * Introduce directory structure and stub modules for MUSICA, and more broadly,
   for chemistry options in the atmosphere core. (PR #1360)

   New directories and modules include:

    src/
      core_atmosphere/
        chemistry/              <--|
          mpas_atm_chemistry.F  <--|
          musica/               <--| new in this release
            mpas_musica.F       <--|

Infrastructure:

 * Introduce the ability to partition meshes "online" at model startup using the
   PT-Scotch library. (PR #1364)

 * Enable execution of halo exchanges directly on GPU-resident fields when MPAS
   is linked with an MPI library that is GPU-aware. To enable GPU-aware halo
   exchanges, a new namelist option, config_gpu_aware_mpi, in the &development
   namelist group must be set to true at runtime. (PR #1355)

 * Improve support for using an external ESMF library through a new build
   option, MPAS_ESMF. (PR #1405)

 * Set the default PnetCDF header alignment to 128 KiB when creating new output
   files with SMIOL. This has been found to fix I/O issues when overwriting
   existing model output files under certain conditions. (PR #1386)

 * Fix an issue with macro expansion with newer Intel oneAPI compilers by adding
   a flag for the 'intel' build target to change the order of macro expansion in
   the Fortran pre-processor. This change in macro expansion order fixes an
   issue with some nested macro use in MPAS. (PR #1392)

 * Fix a buffer overflow in the streaminfo_query function in the
   mpas_stream_inquiry module , where the local array c_attname was allocated
   without space for a C null character. (PR #1352)

Author: mgduda

Makefile

@@ -16,11 +16,11 @@ gnu:   # BUILDTARGET GNU Fortran, C, and C++ compilers
 	"CC_SERIAL = gcc" \
 	"CXX_SERIAL = g++" \
 	"FFLAGS_PROMOTION = -fdefault-real-8 -fdefault-double-8" \
-	"FFLAGS_OPT = -std=f2008 -O3 -ffree-line-length-none -fconvert=big-endian -ffree-form" \
+	"FFLAGS_OPT = -std=f2008 -fimplicit-none -O3 -ffree-line-length-none -fconvert=big-endian -ffree-form" \
 	"CFLAGS_OPT = -O3" \
 	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
-	"FFLAGS_DEBUG = -std=f2008 -g -ffree-line-length-none -fconvert=big-endian -ffree-form -fcheck=all -fbacktrace -ffpe-trap=invalid,zero,overflow" \
+	"FFLAGS_DEBUG = -std=f2008 -fimplicit-none -g -ffree-line-length-none -fconvert=big-endian -ffree-form -fcheck=all -fbacktrace -ffpe-trap=invalid,zero,overflow" \
 	"CFLAGS_DEBUG = -g" \
 	"CXXFLAGS_DEBUG = -g" \
 	"LDFLAGS_DEBUG = -g" \
@@ -663,11 +663,11 @@ intel:   # BUILDTARGET Intel oneAPI Fortran, C, and C++ compiler suite
 	"CC_SERIAL = icx" \
 	"CXX_SERIAL = icpx" \
 	"FFLAGS_PROMOTION = -real-size 64" \
-	"FFLAGS_OPT = -O3 -convert big_endian -free -align array64byte" \
+	"FFLAGS_OPT = -O3 -convert big_endian -free -align array64byte -Qoption,fpp,-macro_expand=vc" \
 	"CFLAGS_OPT = -O3" \
 	"CXXFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
-	"FFLAGS_DEBUG = -g -convert big_endian -free -check bounds,pointers,arg_temp_created,format,shape,contiguous -fpe0 -traceback" \
+	"FFLAGS_DEBUG = -g -convert big_endian -free -check bounds,pointers,arg_temp_created,format,shape,contiguous -fpe0 -traceback -Qoption,fpp,-macro_expand=vc" \
 	"CFLAGS_DEBUG = -g -traceback" \
 	"CXXFLAGS_DEBUG = -g -traceback" \
 	"LDFLAGS_DEBUG = -g -traceback" \
@@ -685,6 +685,24 @@ CPPINCLUDES =
 FCINCLUDES =
 LIBS =
 
+export MPAS_ESMF ?= embedded
+ifeq "$(MPAS_ESMF)" "external"
+  ifeq ($(wildcard $(ESMFMKFILE)), )
+    $(error ESMFMKFILE must be set if MPAS_ESMF=external)
+  endif
+  include $(ESMFMKFILE)
+  export MPAS_ESMF_INC = $(ESMF_F90COMPILEPATHS)
+  export MPAS_ESMF_LIB = $(ESMF_F90LINKPATHS) $(ESMF_F90ESMFLINKPATHS) $(ESMF_F90ESMFLINKLIBS)
+  override CPPFLAGS += -DMPAS_EXTERNAL_ESMF_LIB=true
+  ESMF_MESSAGE="MPAS was built with an external ESMF library using ESMFMKFILE"
+else ifeq "$(MPAS_ESMF)" "embedded"
+  export MPAS_ESMF_INC = -I$(PWD)/src/external/esmf_time_f90
+  export MPAS_ESMF_LIB = -L$(PWD)/src/external/esmf_time_f90 -lesmf_time
+  ESMF_MESSAGE="MPAS was built with the embedded ESMF timekeeping library."
+else
+  $(error Invalid MPAS_ESMF option: $(MPAS_ESMF) - valid options "embedded", "external")
+endif
+
 ifneq "$(PIO)" ""
 #
 # Regardless of PIO library version, look for a lib subdirectory of PIO path
@@ -759,6 +777,15 @@ endif
 	LIBS += $(NCLIB)
 endif
 
+ifneq "$(SCOTCH)" ""
+	SCOTCH_INCLUDES += -I$(SCOTCH)/include
+	SCOTCH_LIBS += -L$(SCOTCH)/lib64 -lptscotch -lscotch  -lptscotcherr -lm
+	SCOTCH_FLAGS = -DMPAS_SCOTCH
+
+	CPPINCLUDES += $(SCOTCH_INCLUDES)
+	LIBS += $(SCOTCH_LIBS)
+	override CPPFLAGS += $(SCOTCH_FLAGS)
+endif
 
 ifneq "$(PNETCDF)" ""
 ifneq ($(wildcard $(PNETCDF)/lib/libpnetcdf.*), )
@@ -872,6 +899,20 @@ $(if $(PRECISION),$(info NOTE: PRECISION=single is unnecessary, single is the de
 	PRECISION_MESSAGE="MPAS was built with default single-precision reals."
 endif #PRECISION IF
 
+# Optional MUSICA support for chemistry
+ifeq "$(shell echo $(MUSICA) | tr '[:upper:]' '[:lower:]')" "true"
+ifeq ($(shell pkg-config --exists musica-fortran && echo yes || echo no), no)
+$(error "musica-fortran package is not installed. Please install it to proceed.")
+endif
+	MUSICA_FCINCLUDES += $(shell pkg-config --cflags musica-fortran)
+	MUSICA_LIBS += $(shell pkg-config --libs musica-fortran)
+	MUSICA_FFLAGS = -DMPAS_USE_MUSICA
+
+	FCINCLUDES += $(MUSICA_FCINCLUDES)
+	LIBS += $(MUSICA_LIBS)
+	override CPPFLAGS += $(MUSICA_FFLAGS)
+endif
+
 ifeq "$(USE_PAPI)" "true"
 	CPPINCLUDES += -I$(PAPI)/include -D_PAPI
 	FCINCLUDES += -I$(PAPI)/include
@@ -1374,6 +1415,63 @@ mpi_f08_test:
 	$(if $(findstring 1,$(MPAS_MPI_F08)), $(eval MPI_F08_MESSAGE = "Using the mpi_f08 module."), )
 	$(if $(findstring 1,$(MPAS_MPI_F08)), $(info mpi_f08 module detected.))
 
+musica_fortran_test:
+	@#
+	@# Create a Fortran test program that will link against the MUSICA library
+	@#
+	$(info Checking for a working MUSICA-Fortran library...)
+	$(eval MUSICA_FORTRAN_TEST := $(shell $\
+		printf "program test_musica_fortran\n$\
+		&   use musica_util, only : string_t\n$\
+		&   use musica_micm, only : get_micm_version\n$\
+		&   type(string_t) :: version_string\n$\
+		&   version_string = get_micm_version()\n$\
+		&   print *, \"MUSICA support is available. MICM version: \", version_string%%value_\n$\
+		end program test_musica_fortran\n" | sed 's/&/ /' > test_musica_fortran.f90; $\
+		$\
+		$(FC) $(MUSICA_FCINCLUDES) $(MUSICA_FFLAGS) test_musica_fortran.f90 -o test_musica_fortran.x $(MUSICA_LIBS) > /dev/null 2>&1; $\
+		musica_fortran_status=$$?; $\
+		rm -f test_musica_fortran.f90 test_musica_fortran.x; $\
+		if [ $$musica_fortran_status -eq 0 ]; then $\
+			printf "1"; $\
+		else $\
+			printf "0"; $\
+		fi $\
+	))
+	$(if $(findstring 0,$(MUSICA_FORTRAN_TEST)), $(error Could not build a simple test program with MUSICA-Fortran))
+	$(eval MUSICA_FORTRAN_VERSION := $(shell pkg-config --modversion musica-fortran))
+	$(if $(findstring 1,$(MUSICA_FORTRAN_TEST)), $(info Built a simple test program with MUSICA-Fortran version $(MUSICA_FORTRAN_VERSION)), )
+
+scotch_c_test:
+	@#
+	@# Create a C test program and try to build against the PT-SCOTCH library
+	@#
+	$(info Checking for a working Scotch library...)
+	$(eval SCOTCH_C_TEST := $(shell $\
+	    printf "#include <stdio.h>\n\
+			&#include \"mpi.h\"\n\
+			&#include \"ptscotch.h\"\n\
+			&int main(){\n\
+			&    int err;\n\
+			&    SCOTCH_Dgraph *dgraph;\n\
+			&    err = SCOTCH_dgraphInit(dgraph, MPI_COMM_WORLD);\n\
+			&    SCOTCH_dgraphExit(dgraph);\n\
+			&    return err;\n\
+			&}\n" | sed 's/&/ /' > ptscotch_c_test.c; $\
+		$\
+		$(CC) $(CPPINCLUDES) $(CFLAGS) $(LDFLAGS) ptscotch_c_test.c -o ptscotch_c_test.x $(SCOTCH_LIBS) > ptscotch_c_test.log 2>&1; $\
+		scotch_c_status=$$?; $\
+		if [ $$scotch_c_status -eq 0 ]; then $\
+			printf "1"; $\
+			rm -f ptscotch_c_test.c ptscotch_c_test.x ptscotch_c_test.log; $\
+		else $\
+			printf "0"; $\
+		fi $\
+	))
+	$(if $(findstring 0,$(SCOTCH_C_TEST)), $(error Could not build a simple C program with Scotch. $\
+		Test program ptscotch_c_test.c and output ptscotch_c_test.log have been left $\
+	    in the top-level MPAS directory for further debugging ))
+	$(if $(findstring 1,$(SCOTCH_C_TEST)), $(info Built a simple C program with Scotch ))
 
 pnetcdf_test:
 	@#
@@ -1424,6 +1522,20 @@ IO_MESSAGE = "Using the SMIOL library."
 override CPPFLAGS += "-DMPAS_SMIOL_SUPPORT"
 endif
 
+ifneq "$(MUSICA_FFLAGS)" ""
+MAIN_DEPS += musica_fortran_test
+MUSICA_MESSAGE = "MPAS was linked with the MUSICA-Fortran library version $(MUSICA_FORTRAN_VERSION)."
+else
+MUSICA_MESSAGE = "MPAS was not linked with the MUSICA-Fortran library."
+endif
+
+ifneq "$(SCOTCH)" ""
+MAIN_DEPS += scotch_c_test
+SCOTCH_MESSAGE = "MPAS has been linked with the Scotch graph partitioning library."
+else
+SCOTCH_MESSAGE = "MPAS was NOT linked with the Scotch graph partitioning library."
+endif
+
 mpas_main: $(MAIN_DEPS)
 	cd src; $(MAKE) FC="$(FC)" \
                  CC="$(CC)" \
@@ -1460,13 +1572,16 @@ mpas_main: $(MAIN_DEPS)
 	@echo $(OPENMP_MESSAGE)
 	@echo $(OPENMP_OFFLOAD_MESSAGE)
 	@echo $(OPENACC_MESSAGE)
+	@echo $(MUSICA_MESSAGE)
+	@echo $(SCOTCH_MESSAGE)
 	@echo $(SHAREDLIB_MESSAGE)
 ifeq "$(AUTOCLEAN)" "true"
 	@echo $(AUTOCLEAN_MESSAGE)
 endif
 	@echo $(GEN_F90_MESSAGE)
 	@echo $(TIMER_MESSAGE)
 	@echo $(IO_MESSAGE)
+	@echo $(ESMF_MESSAGE)
 	@echo "*******************************************************************************"
 clean:
 	cd src; $(MAKE) clean RM="$(RM)" CORE="$(CORE)" AUTOCLEAN="$(AUTOCLEAN)"
@@ -1523,6 +1638,9 @@ errmsg:
 	@echo "    OPENACC=true  - builds and links with OpenACC flags. Default is to not use OpenACC."
 	@echo "    PRECISION=double - builds with default double-precision real kind. Default is to use single-precision."
 	@echo "    SHAREDLIB=true - generate position-independent code suitable for use in a shared library. Default is false."
+	@echo "    MPAS_ESMF=opt  - Selects the ESMF library to be used for MPAS. Options are:"
+	@echo "                     MPAS_ESMF=embedded - Use the embedded ESMF timekeeping library (default)"
+	@echo "                     MPAS_ESMF=external - Use an external ESMF library, determined by ESMFMKFILE"
 	@echo ""
 	@echo "Ensure that NETCDF, PNETCDF, PIO, and PAPI (if USE_PAPI=true) are environment variables"
 	@echo "that point to the absolute paths for the libraries."

README.md

@@ -1,4 +1,4 @@
-MPAS-v8.3.1
+MPAS-v8.4.0
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for

cmake/Functions/MPAS_Functions.cmake

@@ -121,6 +121,7 @@ function(mpas_fortran_target target)
         list(APPEND MPAS_FORTRAN_TARGET_COMPILE_OPTIONS_PUBLIC
                 $<$<COMPILE_LANGUAGE:Fortran>:-align array64byte>
                 $<$<COMPILE_LANGUAGE:Fortran>:-convert big_endian>
+                $<$<COMPILE_LANGUAGE:Fortran>:-Qoption,fpp,-macro_expand=vc>
         )
         if(MPAS_DOUBLE_PRECISION)
             list(APPEND MPAS_FORTRAN_TARGET_COMPILE_OPTIONS_PRIVATE

cmake/Modules/FindPnetCDF.cmake

@@ -133,27 +133,29 @@ set(_new_components)
 if(PnetCDF_Fortran_FOUND AND NOT TARGET PnetCDF::PnetCDF_Fortran)
     add_library(PnetCDF::PnetCDF_Fortran INTERFACE IMPORTED)
     set_target_properties(PnetCDF::PnetCDF_Fortran PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${PnetCDF_INCLUDE_DIR}
-                                                              INTERFACE_LINK_DIRECTORIES ${PnetCDF_LIB_DIR})
+                                                              INTERFACE_LINK_DIRECTORIES ${PnetCDF_LIB_DIR}
+                                                              INTERFACE_LINK_LIBRARIES pnetcdf)
     if(PnetCDF_MODULE_DIR AND NOT PnetCDF_MODULE_DIR STREQUAL PnetCDF_INCLUDE_DIR )
         set_property(TARGET PnetCDF::PnetCDF_Fortran APPEND PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${PnetCDF_MODULE_DIR})
     endif()
     set(_new_components 1)
-    target_link_libraries(PnetCDF::PnetCDF_Fortran INTERFACE -lpnetcdf)
 endif()
 
 # PnetCDF::PnetCDF_C imported interface target
 if(PnetCDF_C_FOUND AND NOT TARGET PnetCDF::PnetCDF_C)
     add_library(PnetCDF::PnetCDF_C INTERFACE IMPORTED)
     set_target_properties(PnetCDF::PnetCDF_C PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${PnetCDF_INCLUDE_DIR}
-                                                        INTERFACE_LINK_DIRECTORIES ${PnetCDF_LIB_DIR})
+                                                        INTERFACE_LINK_DIRECTORIES ${PnetCDF_LIB_DIR}
+                                                        INTERFACE_LINK_LIBRARIES pnetcdf)
     set(_new_components 1)
 endif()
 
 # PnetCDF::PnetCDF_CXX imported interface target
 if(PnetCDF_CXX_FOUND AND NOT TARGET PnetCDF::PnetCDF_CXX)
     add_library(PnetCDF::PnetCDF_CXX INTERFACE IMPORTED)
     set_target_properties(PnetCDF::PnetCDF_CXX PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${PnetCDF_INCLUDE_DIR}
-                                                          INTERFACE_LINK_DIRECTORIES ${PnetCDF_LIB_DIR})
+                                                          INTERFACE_LINK_DIRECTORIES ${PnetCDF_LIB_DIR}
+                                                          INTERFACE_LINK_LIBRARIES pnetcdf)
     set(_new_components 1)
 endif()
 

src/Makefile

@@ -9,7 +9,7 @@ else
 all: mpas
 
 mpas: $(AUTOCLEAN_DEPS) externals frame ops dycore drver
-	$(LINKER) $(LDFLAGS) -o $(EXE_NAME) driver/*.o -L. -ldycore -lops -lframework $(LIBS) -I./external/esmf_time_f90 -L./external/esmf_time_f90 -lesmf_time
+	$(LINKER) $(LDFLAGS) -o $(EXE_NAME) driver/*.o -L. -ldycore -lops -lframework $(LIBS) $(MPAS_ESMF_INC) $(MPAS_ESMF_LIB)
 
 externals: $(AUTOCLEAN_DEPS)
 	( cd external; $(MAKE) FC="$(FC)" SFC="$(SFC)" CC="$(CC)" SCC="$(SCC)" FFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" CPP="$(CPP)" NETCDF="$(NETCDF)" CORE="$(CORE)" all )

src/core_atmosphere/CMakeLists.txt

@@ -97,20 +97,16 @@ set(ATMOSPHERE_CORE_PHYSICS_WRF_SOURCES
 list(TRANSFORM ATMOSPHERE_CORE_PHYSICS_WRF_SOURCES PREPEND physics/physics_wrf/)
 
 
-set(ATMOSPHERE_CORE_PHYSICS_MMM_DIR ${CMAKE_CURRENT_SOURCE_DIR}/physics/physics_mmm)
-
-if(NOT EXISTS ${ATMOSPHERE_CORE_PHYSICS_MMM_DIR})
-    set(PHYSICS_MMM_REPO_URL "https://github.com/NCAR/MMM-physics")
-    execute_process(COMMAND git clone ${PHYSICS_MMM_REPO_URL} ${ATMOSPHERE_CORE_PHYSICS_MMM_DIR}
-                    RESULT_VARIABLE GIT_CLONE_RESULT
-                    OUTPUT_VARIABLE GIT_CLONE_OUTPUT
-                    ERROR_VARIABLE GIT_CLONE_ERROR)
-    if(NOT GIT_CLONE_RESULT EQUAL 0)
-        message(FATAL_ERROR "Git clone failed with error: ${GIT_CLONE_ERROR}")
-    endif()
-
+set(CHECKOUT ${CMAKE_CURRENT_SOURCE_DIR}/tools/manage_externals/checkout_externals )
+execute_process( COMMAND
+                 ${CHECKOUT} --externals ${CMAKE_CURRENT_SOURCE_DIR}/Externals.cfg
+                 WORKING_DIRECTORY       ${CMAKE_CURRENT_SOURCE_DIR}/physics/
+                 RESULT_VARIABLE         MANAGE_EXTERNALS_STATUS
+                )
+if ( ${MANAGE_EXTERNALS_STATUS} AND NOT ${MANAGE_EXTERNALS_STATUS} EQUAL 0 )
+    message( FATAL_ERROR "Failed to checkout external repos via manage_externals" )
 else()
-    message(STATUS "Directory ${DIR_TO_CHECK} already exists, skipping clone")
+    message( STATUS "Finished checking out external repos via manage_externals" )
 endif()
 
 set(ATMOSPHERE_CORE_PHYSICS_MMM_SOURCES
@@ -130,22 +126,6 @@ set(ATMOSPHERE_CORE_PHYSICS_MMM_SOURCES
 
 list(TRANSFORM ATMOSPHERE_CORE_PHYSICS_MMM_SOURCES PREPEND physics/physics_mmm/)
 
-set(ATMOSPHERE_CORE_PHYSICS_NOAA_DIR ${CMAKE_CURRENT_SOURCE_DIR}/physics/physics_noaa/UGWP)
-
-if(NOT EXISTS ${ATMOSPHERE_CORE_PHYSICS_NOAA_DIR})
-    set(PHYSICS_NOAA_REPO_URL "https://github.com/NOAA-GSL/UGWP.git")
-    execute_process(COMMAND git clone ${PHYSICS_NOAA_REPO_URL} ${ATMOSPHERE_CORE_PHYSICS_NOAA_DIR}
-                    RESULT_VARIABLE GIT_CLONE_RESULT
-                    OUTPUT_VARIABLE GIT_CLONE_OUTPUT
-                    ERROR_VARIABLE GIT_CLONE_ERROR)
-    if(NOT GIT_CLONE_RESULT EQUAL 0)
-        message(FATAL_ERROR "Git clone failed with error: ${GIT_CLONE_ERROR}")
-    endif()
-
-else()
-    message(STATUS "Directory ${DIR_TO_CHECK} already exists, skipping clone")
-endif()
-
 set(ATMOSPHERE_CORE_PHYSICS_NOAA_SOURCES
     bl_ugwp.F
     bl_ugwpv1_ngw.F
@@ -335,6 +315,7 @@ list(TRANSFORM ATMOSPHERE_CORE_DIAGNOSTIC_SOURCES PREPEND diagnostics/)
 # dynamics/
 set(ATMOSPHERE_CORE_DYNAMICS_SOURCES
     mpas_atm_boundaries.F
+    mpas_atm_dissipation_models.F
     mpas_atm_iau.F
     mpas_atm_time_integration.F)
 list(TRANSFORM ATMOSPHERE_CORE_DYNAMICS_SOURCES PREPEND dynamics/)