Feature/aqm canopy

README

@@ -1 +1,2 @@
-
+Modified branch to account for in-canopy effects on composition/weather
+Export 5 2D canopy data fields and 3 2D photolysis diagnostics (I. Ivanova, 02/14/2024)

aqm_files.cmake

@@ -187,7 +187,6 @@ 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
@@ -243,4 +242,6 @@ list(APPEND aqm_CCTM_files
 	${localCCTM}/ASX_DATA_MOD.F
 	${localCCTM}/DUST_EMIS.F
 	${localCCTM}/AERO_PHOTDATA.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 options:
 #
@@ -83,7 +108,7 @@ ctm_stdout: all
 emission_sources: myemis
 
 #
-#  Emission type: anthropogenic, biogenic, gbbepx, fengsha
+#  Emission type: anthropogenic, biogenic, gbbepx, fengsha, canopy
 #
 myemis_type: anthropogenic
 

src/aqm_cap.F90

@@ -9,11 +9,12 @@ module AQM
 
   use aqm_comp_mod
   use aqm_const_mod, only: rad_to_deg
-  
+
   implicit none
 
   ! -- import fields
   integer, parameter :: importFieldCount = 36
+!  integer, parameter :: importFieldCount = 45  !with canopy
   character(len=*), dimension(importFieldCount), parameter :: &
     importFieldNames = (/ &
       "canopy_moisture_storage                  ", &
@@ -52,30 +53,47 @@ 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
+  integer, parameter :: exportFieldCount = 2+3+5  !IVAI: add 3 photolysis inst_tracer_diag_* and five canopy variables
   character(len=*), dimension(exportFieldCount), parameter :: &
     exportFieldNames = (/ &
       "inst_tracer_mass_frac                ", &
-      "inst_tracer_diag_aod                 "  &
+      "inst_tracer_diag_aod                 ", &
+      "inst_tracer_diag_claie               ", & !IVAI: canopy via aqm_emis_read
+      "inst_tracer_diag_cfch                ", & !IVAI: canopy via aqm_emis_read
+      "inst_tracer_diag_cfrt                ", & !IVAI: canopy via aqm_emis_read
+      "inst_tracer_diag_cclu                ", & !IVAI: canopy via aqm_emis_read
+      "inst_tracer_diag_cpopu               ", & !IVAI: canopy via aqm_emis_read
+      "inst_tracer_diag_coszens             ", & !IVAI: photdiag
+      "inst_tracer_diag_jo3o1d              ", & !IVAI: photdiag
+      "inst_tracer_diag_jno2                "  & !IVAI: photdiag
     /)
 
   private
 
   public SetServices
-  
+
   !-----------------------------------------------------------------------------
   contains
   !-----------------------------------------------------------------------------
-  
+
   subroutine SetServices(model, rc)
     type(ESMF_GridComp)  :: model
     integer, intent(out) :: rc
 
     ! begin
     rc = ESMF_SUCCESS
-    
+
     ! the NUOPC model component will register the generic methods
     call NUOPC_CompDerive(model, inheritModel, rc=rc)
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
@@ -120,15 +138,15 @@ subroutine SetServices(model, rc)
       return  ! bail out
 
   end subroutine
-  
+
   !-----------------------------------------------------------------------------
 
   subroutine InitializeP0(model, importState, exportState, clock, rc)
     type(ESMF_GridComp)  :: model
     type(ESMF_State)     :: importState, exportState
     type(ESMF_Clock)     :: clock
     integer, intent(out) :: rc
-    
+
     ! local variables
     integer                    :: verbosity
     character(len=ESMF_MAXSTR) :: msgString, name, rcFile
@@ -195,16 +213,16 @@ subroutine InitializeP0(model, importState, exportState, clock, rc)
       line=__LINE__, &
       file=__FILE__)) &
       return  ! bail out
-    
+
   end subroutine
-  
+
   !-----------------------------------------------------------------------------
   subroutine InitializeP1(model, importState, exportState, clock, rc)
     type(ESMF_GridComp)  :: model
     type(ESMF_State)     :: importState, exportState
     type(ESMF_Clock)     :: clock
     integer, intent(out) :: rc
-    
+
     ! begin
     rc = ESMF_SUCCESS
 
@@ -285,7 +303,7 @@ subroutine DataInitialize(model, rc)
       return  ! bail out
 
     ! -- check if import fields are defined
-    if (importFieldCount < 1) then 
+    if (importFieldCount < 1) then
       call ESMF_LogSetError(ESMF_RC_NOT_IMPL, &
         msg="This component requires import fields to be defined.", &
         line=__LINE__, file=__FILE__, &
@@ -294,7 +312,7 @@ subroutine DataInitialize(model, rc)
     end if
 
     ! -- check if export fields are defined
-    if (exportFieldCount < 1) then 
+    if (exportFieldCount < 1) then
       call ESMF_LogSetError(ESMF_RC_NOT_IMPL, &
         msg="This component requires export fields to be defined.", &
         line=__LINE__, file=__FILE__, &
@@ -417,7 +435,7 @@ subroutine DataInitialize(model, rc)
             line=__LINE__, &
             file=__FILE__)) &
             return  ! bail out
-         
+
         do item = 1, 2
           call ESMF_GridGetCoord(grid, coordDim=item, staggerloc=ESMF_STAGGERLOC_CENTER, &
             localDE=localDe, farrayPtr=coord, rc=rc)
@@ -534,7 +552,7 @@ end subroutine DataInitialize
   subroutine ModelAdvance(model, rc)
     type(ESMF_GridComp)  :: model
     integer, intent(out) :: rc
-    
+
     ! local variables
     type(ESMF_Clock)              :: clock
     type(ESMF_State)              :: importState, exportState
@@ -548,7 +566,7 @@ subroutine ModelAdvance(model, rc)
 
     ! begin
     rc = ESMF_SUCCESS
-    
+
     ! get component's information
     call NUOPC_CompGet(model, name=name, diagnostic=diagnostic, rc=rc)
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &

src/aqm_comp_mod.F90

@@ -325,6 +325,57 @@ subroutine aqm_comp_export(state, fieldNames, rc)
               line=__LINE__, &
               file=__FILE__)) &
               return  ! bail
+!IVAI: canopy fields read in via 'aqm_emiss_read'
+          case ("inst_tracer_diag_claie")
+            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateOut % claie, rc=rc)
+            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+              line=__LINE__, &
+              file=__FILE__)) &
+              return  ! bail
+          case ("inst_tracer_diag_cfch")
+            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateOut % cfch, rc=rc)
+            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+              line=__LINE__, &
+              file=__FILE__)) &
+              return  ! bail
+          case ("inst_tracer_diag_cfrt")
+            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateOut % cfrt, rc=rc)
+            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+              line=__LINE__, &
+              file=__FILE__)) &
+              return  ! bail
+          case ("inst_tracer_diag_cclu")
+            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateOut % cclu, rc=rc)
+            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+              line=__LINE__, &
+              file=__FILE__)) &
+              return  ! bail
+          case ("inst_tracer_diag_cpopu")
+            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateOut % cpopu, rc=rc)
+            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+              line=__LINE__, &
+              file=__FILE__)) &
+              return  ! bail
+!IVAI: photdiag CTM_RJ_1 fields
+          case ("inst_tracer_diag_coszens")
+            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateOut % coszens, rc=rc)
+            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+              line=__LINE__, &
+              file=__FILE__)) &
+              return  ! bail
+          case ("inst_tracer_diag_jo3o1d")
+            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateOut % jo3o1d, rc=rc)
+            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+              line=__LINE__, &
+              file=__FILE__)) &
+              return  ! bail
+          case ("inst_tracer_diag_jno2")
+            call ESMF_FieldGet(field, localDe=localDe, farrayPtr=stateOut % jno2, rc=rc)
+            if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, &
+              line=__LINE__, &
+              file=__FILE__)) &
+              return  ! bail
+!IVAI
           case default
             ! -- unused field
         end select
@@ -605,6 +656,61 @@ 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

src/model/Makefile.am

@@ -168,7 +168,6 @@ libCCTM_a_SOURCES += \
 	$(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 \
@@ -219,7 +218,6 @@ libCCTM_a_SOURCES += \
 	$(UTIL)/bmatvec.F \
 	$(UTIL)/findex.f \
 	$(UTIL)/get_envlist.f \
-	$(UTIL)/setup_logdev.F \
 	$(UTIL)/subhdomain.F \
 	$(UTIL)/UTILIO_DEFN.F
 
@@ -250,11 +248,11 @@ libCCTM_a_SOURCES += \
 	${localCCTM}/PT3D_DEFN.F \
 	${localCCTM}/PT3D_FIRE_DEFN.F \
 	${localCCTM}/PT3D_STKS_DEFN.F \
+	$(localCCTM)/phot.F \
 	${localCCTM}/ASX_DATA_MOD.F \
+	$(localCCTM)/centralized_io_util_module.F \
 	${localCCTM}/DUST_EMIS.F \
 	${localCCTM}/AERO_PHOTDATA.F
-
-
 libCCTM_a_CPPFLAGS  = -DSUBST_FILES_ID=\"FILES_CTM.EXT\"
 libCCTM_a_CPPFLAGS += -DSUBST_CONST=\"CONST.EXT\"
 libCCTM_a_CPPFLAGS += -DSUBST_EMISPRM=\"EMISPRM.EXT\"
@@ -432,6 +430,10 @@ $(libEMIS)BIOG_EMIS.$(OBJEXT) : \
 	$(libUTIL)UTILIO_DEFN.$(OBJEXT)
 $(libEMIS)cropcal.$(OBJEXT) : \
 	$(libGRID)HGRD_DEFN.$(OBJEXT) $(libUTIL)UTILIO_DEFN.$(OBJEXT)
+$(libEMIS)DUST_EMIS.$(OBJEXT) : $(ICL)/const/CONST.EXT $(ICL)/filenames/FILES_CTM.EXT \
+	$(libAERO)AERO_DATA.$(OBJEXT) $(liblocalCCTM)ASX_DATA_MOD.$(OBJEXT) \
+	$(libGRID)GRID_CONF.$(OBJEXT) $(libGRID)HGRD_DEFN.$(OBJEXT) \
+	$(libEMIS)LUS_DEFN.$(OBJEXT) $(libUTIL)UTILIO_DEFN.$(OBJEXT)
 $(libEMIS)EMIS_DEFN.$(OBJEXT) : $(ICL)/const/CONST.EXT $(ICL)/filenames/FILES_CTM.EXT \
 	$(libAERO)AERO_DATA.$(OBJEXT) $(libAERO)AERO_EMIS.$(OBJEXT) \
 	$(liblocalCCTM)ASX_DATA_MOD.$(OBJEXT) $(libEMIS)BEIS_DEFN.$(OBJEXT) \