Feature/aqm canopy merge to develop

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "src/model/CMAQ"]
 	path = src/model/CMAQ
-	url = https://github.com/NOAA-EMC/CMAQ
-	branch = dev/emc
+	url = https://github.com/USEPA/CMAQ
+	branch = 5.2.1

CMakeLists.txt

@@ -50,7 +50,8 @@ target_include_directories(drv PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_
                                        $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/src/io/aqmio>
                                        $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/src/model>)
 target_compile_definitions(drv PUBLIC verbose_driver)
-target_link_libraries(drv PRIVATE shr CCTM esmf)
+#target_link_libraries(drv PRIVATE shr CCTM esmf)
+target_link_libraries(drv PRIVATE shr CCTM)
 
 # src/io/aqmio
 add_library(aqmio OBJECT ${aqm_aqmio_files})
@@ -86,6 +87,8 @@ target_compile_definitions(CCTM PUBLIC SUBST_FILES_ID="FILES_CTM.EXT"
                                        SUBST_BARRIER=NOOP_BARRIER
                                        SUBST_SUBGRID_INDEX=NOOP_SUBGRID_INDEX
                                        EDDYX=DUMMY_EDDYX
+                                       MOSAIC_MOD=MOSAIC_MODULE
+                                       Mosaic_Mod=Mosaic_Module
                                        OPCONC=DUMMY_OPCONC
 				       OPACONC=DUMMY_OPACONC
                                        OPWDEP=DUMMY_OPWDEP
@@ -94,7 +97,6 @@ target_compile_definitions(CCTM PUBLIC SUBST_FILES_ID="FILES_CTM.EXT"
 				       verbose_gas
                                        mpas
 				       _AQM_)
-target_link_libraries(CCTM PRIVATE esmf)
 
 # AQM
 add_library(aqm STATIC ${aqm_files} $<TARGET_OBJECTS:shr>
@@ -103,6 +105,12 @@ add_library(aqm STATIC ${aqm_files} $<TARGET_OBJECTS:shr>
                          	    $<TARGET_OBJECTS:ioapi>
                          	    $<TARGET_OBJECTS:CCTM>)
 set_target_properties(aqm PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
+add_custom_target(aqm_mosaic
+                  COMMAND ${CMAKE_COMMAND} -E create_symlink
+                          ${CMAKE_CURRENT_BINARY_DIR}/mod/mosaic_module.mod
+                          ${CMAKE_CURRENT_BINARY_DIR}/mod/mosaic_mod.mod
+                  )
+add_dependencies(aqm aqm_mosaic)
 add_library(aqm::aqm ALIAS aqm)
 target_include_directories(aqm PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
                                       $<INSTALL_INTERFACE:mod>)

README

@@ -1 +1 @@
-
+Modified branch to account for in-canopy effects on composition/weather

aqm_files.cmake

@@ -130,7 +130,6 @@ list(APPEND aqm_CCTM_files
 	${EMIS}/BEIS_DEFN.F
 	${EMIS}/BIOG_EMIS.F
 	${EMIS}/cropcal.F
-	${EMIS}/DUST_EMIS.F
 	${EMIS}/EMIS_DEFN.F
 	${EMIS}/LTNG_DEFN.F
 	${EMIS}/LUS_DEFN.F
@@ -180,7 +179,6 @@ list(APPEND aqm_CCTM_files
 	${PHOT}/CSQY_DATA.F
 	${PHOT}/OMI_1979_to_2015.dat
 	${PHOT}/opphot.F
-	${PHOT}/phot.F
 	${PHOT}/PHOT_MET_DATA.F
 	${PHOT}/PHOT_MOD.F
 	${PHOT}/PHOTOLYSIS_ALBEDO.F
@@ -215,7 +213,6 @@ list(APPEND aqm_CCTM_files
 	${UTIL}/subhdomain.F
 	${UTIL}/UTILIO_DEFN.F
 	${VDIFF}/aero_sedv.F
-	${VDIFF}/ASX_DATA_MOD.F
 	${VDIFF}/conv_cgrid.F
 	${VDIFF}/matrix1.F
 	${VDIFF}/opddep.F
@@ -231,4 +228,8 @@ list(APPEND aqm_CCTM_files
 	${localCCTM}/vdiffacmx.F
 	${localCCTM}/PTMAP.F
 	${localCCTM}/PT3D_DEFN.F
+        ${localCCTM}/ASX_DATA_MOD.F
+        ${localCCTM}/DUST_EMIS.F
+        ${localCCTM}/phot.F
+        ${localCCTM}/centralized_io_util_module.F
 )

examples/aqm.rc

@@ -34,6 +34,31 @@ omi_data:    /scratch1/NCEPDEV/nems/Raffaele.Montuoro/dev/aqm/epa/data/omi_cmaq_
 # - set to true for cold start
 init_concentrations: true
 
+#
+# Inline Canopy Effects
+#
+canopy_yn: true
+
+canopy_type: canopy
+
+canopy_format: netcdf
+
+canopy_file: /scratch2/NAGAPE/arl/Patrick.C.Campbell/canopy_geofiles/gfs.t12z.geo.08.canopy_regrid.nc
+
+canopy_frequency: static
+
+canopy_species::
+    FCH        1.00000   FCH      m
+    FRT        1.00000   FRT      1
+    CLU        1.00000   CLU      1
+    POPU       1.00000   POPU     10000_people/10km2
+    LAIE       1.00000   LAIE     1
+    C1R        1.00000   C1R      1
+    C2R        1.00000   C2R      1
+    C3R        1.00000   C3R      1
+    C4R        1.00000   C4R      1
+::
+
 #
 # Run aerosol module
 #
@@ -55,6 +80,20 @@ ctm_aod: true
 #  Compute and export PM2.5 mode fractions as diagnostic tracers
 ctm_pmdiag: true
 
+#
+# Fengsha Dust Emission Option
+#
+fengsha_yn: true
+
+fengsha_format: netcdf
+
+fengsha_file: /scratch1/RDARCH/rda-arl-gpu/Barry.Baker/emissions/nexus/FENGSHA/FENGSHA_FILES.nc
+
+fengsha_species::
+    clayf      1.00000   clayf    1
+    sandf      1.00000   sandf    1
+    drag       1.00000   drag     1
+    uthr       1.00000   uthr     1
 
 #
 #  Input emissions
@@ -65,7 +104,7 @@ ctm_pmdiag: true
 emission_sources: myemis
 
 #
-#  Emission type: anthropogenic, biogenic, gbbepx
+#  Emission type: anthropogenic, biogenic, gbbepx, canopy
 #
 myemis_type: anthropogenic
 
@@ -194,3 +233,5 @@ myemis_species::
     SESQ
     TOLU
 ::
+
+

src/aqm_cap.F90

@@ -13,6 +13,7 @@ module AQM
 
   ! -- import fields
   integer, parameter :: importFieldCount = 35
+!  integer, parameter :: importFieldCount = 44  !with canopy
   character(len=*), dimension(importFieldCount), parameter :: &
     importFieldNames = (/ &
       "canopy_moisture_storage                  ", &
@@ -50,6 +51,15 @@ module AQM
       "surface_cell_area                        ", &
       "surface_snow_area_fraction               ", &
       "temperature_of_soil_layer                "  &
+!      "forest_canopy_height                     ", &
+!      "forest_fraction                          ", &
+!      "clumping_index                           ", &      
+!      "population_density                       ", &
+!      "leaf_area_index_eccc                     ", &
+!      "cum_lai_frac1_eccc                       ", &
+!      "cum_lai_frac2_eccc                       ", &
+!      "cum_lai_frac3_eccc                       ", &
+!      "cum_lai_frac4_eccc                       ", &
     /)
   ! -- export fields
   integer, parameter :: exportFieldCount = 2

src/aqm_comp_mod.F90

@@ -584,6 +584,61 @@ subroutine aqm_comp_import(state, fieldNames, rc)
               line=__LINE__, &
               file=__FILE__)) &
               return  ! bail
+!canopy variables 
+!          case ("forest_canopy_height")
+!            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateIn % stemp, rc=rc)
+!            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+!              line=__LINE__, &
+!              file=__FILE__)) &
+!              return  ! bail
+!          case ("forest_fraction")
+!            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateIn % stemp, rc=rc)
+!            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+!              line=__LINE__, &
+!              file=__FILE__)) &
+!              return  ! bail
+!          case ("clumping_index")
+!            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateIn % stemp, rc=rc)
+!            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+!              line=__LINE__, &
+!              file=__FILE__)) &
+!              return  ! bail
+!          case ("population_density")
+!            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateIn % stemp, rc=rc)
+!            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+!              line=__LINE__, &
+!              file=__FILE__)) &
+!              return  ! bail
+!          case ("leaf_area_index_eccc")
+!            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateIn % stemp, rc=rc)
+!            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+!              line=__LINE__, &
+!              file=__FILE__)) &
+!              return  ! bail
+!          case ("cum_lai_frac1_eccc")
+!            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateIn % stemp, rc=rc)
+!            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+!              line=__LINE__, &
+!              file=__FILE__)) &
+!              return  ! bail
+!          case ("cum_lai_frac2_eccc")
+!            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateIn % stemp, rc=rc)
+!            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+!              line=__LINE__, &
+!              file=__FILE__)) &
+!              return  ! bail
+!          case ("cum_lai_frac3_eccc")
+!            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateIn % stemp, rc=rc)
+!            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+!              line=__LINE__, &
+!              file=__FILE__)) &
+!              return  ! bail
+!          case ("cum_lai_frac4_eccc")
+!            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateIn % stemp, rc=rc)
+!            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+!              line=__LINE__, &
+!              file=__FILE__)) &
+!              return  ! bail
           case default
             ! -- unused field
         end select