Upgrade CMAQ from 5.2 to 5.4, Use correct variable for LUFRAC_ and DLUSE

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "src/model/CMAQ"]
 	path = src/model/CMAQ
 	url = https://github.com/USEPA/CMAQ
-	branch = 5.2.1
+	branch = 5.4+

CMakeLists.txt

@@ -20,7 +20,8 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
   set(CMAKE_Fortran_FLAGS "-ffree-line-length-none -ffixed-line-length-none")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
   set(CMAKE_Fortran_FLAGS "-extend-source 132")
-  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -check bounds -check uninit -fpe0 -fno-alias -ftrapuv -traceback")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -check all -check noarg_temp_created -fpe0 -fno-alias -ftrapuv -traceback")
+  # set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -check bounds -check uninit -fpe0 -fno-alias -ftrapuv -traceback")
 else()
   message(WARNING "Fortran compiler with ID ${CMAKE_Fortran_COMPILER_ID} will be used with CMake default options")
 endif()
@@ -93,6 +94,7 @@ target_compile_definitions(CCTM PUBLIC SUBST_FILES_ID="FILES_CTM.EXT"
                                        SUBST_PE_COMM="PE_COMM.EXT"
                                        SUBST_COMM=NOOP_COMM
                                        SUBST_BARRIER=NOOP_BARRIER
+                                       SUBST_HI_LO_BND_PE=NOOP_HI_LO_BND_PE
                                        SUBST_SUBGRID_INDEX=NOOP_SUBGRID_INDEX
                                        AQCHEM=DUMMY_AQCHEM
                                        CONVCLD_ACM=DUMMY_CONVCLD_ACM
@@ -105,7 +107,8 @@ target_compile_definitions(CCTM PUBLIC SUBST_FILES_ID="FILES_CTM.EXT"
 				       WR_INIT=DUMMY_WR_INIT
                                        verbose_aero
 				       verbose_gas
-                                       mpas
+                                       verbose_cio
+                                      # mpas
 				       _AQM_)
 
 # AQM

README

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

aqm_files.cmake

@@ -36,6 +36,7 @@ list(APPEND aqm_aqmio_files
 list(APPEND aqm_ioapi_files
     src/io/ioapi/FDESC3.EXT
     src/io/ioapi/PARMS3.EXT
+    src/io/ioapi/IODECL3.EXT
     src/io/ioapi/crlf.F
     src/io/ioapi/currec.f
     src/io/ioapi/currstep.f
@@ -59,62 +60,70 @@ list(APPEND aqm_ioapi_files
     src/io/ioapi/upcase.f
     src/io/ioapi/wkday.F
     src/io/ioapi/yr2day.F
+    src/io/ioapi/daymon.F
     src/io/ioapi/m3exit.F90
     src/io/ioapi/m3mesg.F90
     src/io/ioapi/m3msg2.F90
     src/io/ioapi/m3warn.F90
+    src/io/ioapi/m3err.F
     src/io/ioapi/m3utilio.F90
 )
 
 set(CCTM_ROOT "src/model/CMAQ/CCTM/src")
 set(AERO "${CCTM_ROOT}/aero/aero6")
-set(BIOG "${CCTM_ROOT}/biog/beis3")
+set(BIOG "${CCTM_ROOT}/biog/beis4")
+set(MEGAN "${CCTM_ROOT}/biog/megan3")
 set(CLOUD "${CCTM_ROOT}/cloud/acm_ae6")
 set(DEPV "${CCTM_ROOT}/depv/m3dry")
 set(EMIS "${CCTM_ROOT}/emis/emis")
-set(GAS "${CCTM_ROOT}/gas/ebi_cb6r3_ae6_aq")
+set(GAS "${CCTM_ROOT}/gas/ros3")
 set(GRID "${CCTM_ROOT}/grid/cartesian")
 set(ICL "${CCTM_ROOT}/ICL/fixed")
-set(INIT "${CCTM_ROOT}/init/yamo")
-set(MECHS "${CCTM_ROOT}/MECHS/cb6r3_ae6_aq")
+set(INIT "${CCTM_ROOT}/init")
+set(MECHS "${CCTM_ROOT}/MECHS/cb6r5_ae7_aq")
 set(PA "${CCTM_ROOT}/procan/pa")
 set(PHOT "${CCTM_ROOT}/phot/inline")
 set(PLRISE "${CCTM_ROOT}/plrise/smoke")
 set(SPCS "${CCTM_ROOT}/spcs/cgrid_spcs_nml")
+set(STM "${CCTM_ROOT}/stm")
 set(STENEX "${CCTM_ROOT}/STENEX/noop")
 set(UTIL "${CCTM_ROOT}/util/util")
-set(VDIFF "${CCTM_ROOT}/vdiff/acm2")
+set(VDIFF "${CCTM_ROOT}/vdiff/acm2_m3dry")
+set(DRIV "${CCTM_ROOT}/driver")
+set(CIO "${CCTM_ROOT}/cio")
 set(localCCTM "src/model/src")
 list(APPEND aqm_CCTM_files
 	${AERO}/AERO_DATA.F
 	${AERO}/aero_driver.F
-	${AERO}/AERO_EMIS.F
+        ${AERO}/aero_nml_modes.F
 	${AERO}/AEROMET_DATA.F
+        ${AERO}/AERO_EMIS.F
 	${AERO}/AEROSOL_CHEMISTRY.F
 	${AERO}/aero_subs.F
-	${AERO}/aero_depv.F
-	${AERO}/AOD_DEFN.F
 	${AERO}/coags.f
 	${AERO}/getpar.f
 	${AERO}/isocom.f
 	${AERO}/isofwd.f
 	${AERO}/isorev.f
 	${AERO}/isrpia.inc
-	${AERO}/opvis.F
-	${AERO}/opavis.F
-	${AERO}/oppmdiag.F
-	${AERO}/opapmdiag.F
+        ${AERO}/AERO_BUDGET.F
 	${AERO}/PRECURSOR_DATA.F
-	${AERO}/PMDIAG_DATA.F
 	${AERO}/SOA_DEFN.F
-	${BIOG}/beis3.F
+	${BIOG}/beis.F
 	${BIOG}/checkmem.f
 	${BIOG}/czangle.F
 	${BIOG}/getparb.f
 	${BIOG}/hrno.F
 	${BIOG}/parsline.f
 	${BIOG}/tmpbeis.F
 	${BIOG}/wrdaymsg.f
+        ${MEGAN}/MEGAN_DEFN.F
+        ${MEGAN}/megan_gspro.F
+        ${MEGAN}/megan_hrno_mod.F
+        ${MEGAN}/megan_fx_mod.f90
+        ${MEGAN}/BDSNP_MOD.F
+        ${MEGAN}/MAP_CV2CB6_AE7.EXT
+        ${MEGAN}/SPC_CB6_AE7.EXT
 	${CLOUD}/hlconst.F
 	${CLOUD}/cldproc_acm.F
 	${CLOUD}/getalpha.F
@@ -131,42 +140,43 @@ list(APPEND aqm_CCTM_files
 	${DEPV}/gas_depv_map.F
 	${DEPV}/HGSIM.F
 	${DEPV}/LSM_MOD.F
-	${DEPV}/MOSAIC_MOD.F
+        ${DEPV}/depv_data_module.F
 	${DEPV}/opdepv_diag.F
-	${DEPV}/opdepv_mos.F
-	${DEPV}/opdepv_fst.F
 	${DEPV}/m3dry.F
 	${EMIS}/BEIS_DEFN.F
 	${EMIS}/BIOG_EMIS.F
 	${EMIS}/cropcal.F
-	${EMIS}/EMIS_DEFN.F
+        ${EMIS}/crop_data_module.F
 	${EMIS}/LTNG_DEFN.F
 	${EMIS}/LUS_DEFN.F
 	${EMIS}/MGEMIS.F
-	${EMIS}/opemis.F
 	${EMIS}/PTBILIN.F
 	${EMIS}/SSEMIS.F
 	${EMIS}/STK_EMIS.F
 	${EMIS}/STK_PRMS.F
-	${EMIS}/tfabove.F
-	${EMIS}/tfbelow.F
 	${EMIS}/UDTYPES.F
-	${GAS}/degrade_data.F
-	${GAS}/degrade.F
-	${GAS}/DEGRADE_SETUP_TOX.F
-	${GAS}/final_degrade.F
-	${GAS}/find_degraded.F
-	${GAS}/hrdata_mod.F
-	${GAS}/hrdriver.F
-	${GAS}/hrg1.F
-	${GAS}/hrg2.F
-	${GAS}/hrg3.F
-	${GAS}/hrg4.F
-	${GAS}/hrinit.F
-	${GAS}/hrprodloss.F
-	${GAS}/hrrates.F
-	${GAS}/hrsolver.F
-	${GAS}/init_degrade.F
+        ${EMIS}/biog_emis_param_module.F
+        ${EMIS}/CMAQ_Control_DESID.nml
+        ${EMIS}/desid_param_module.F
+        ${EMIS}/desid_util.F
+        ${EMIS}/desid_vars.F
+        ${EMIS}/desid_module.F
+        ${EMIS}/lus_data_module.F
+        ${EMIS}/stack_group_data_module.F
+      #  ${EMIS}/PT3D_DEFN.F
+        ${EMIS}/PTMET.F
+	${GAS}/../../reactive_tracers/DEGRADE_PARAMETERS.F
+	${GAS}/../../reactive_tracers/DEGRADE_ROUTINES.F
+	${GAS}/rbdata_mod.F
+	#${GAS}/rbdriver.F
+	${GAS}/rbdecomp.F
+	${GAS}/rbfeval.F
+	${GAS}/rbinit.F
+	${GAS}/rbjacob.F
+	${GAS}/rbsolve.F
+	${GAS}/rbsolver.F
+	${GAS}/rbsparse.F
+	${GAS}/../../reactive_tracers/DEGRADE_SETUP_TOX.F
 	${GRID}/GRID_CONF.F
 	${GRID}/HGRD_DEFN.F
 	${GRID}/VGRD_DEFN.F
@@ -181,29 +191,35 @@ list(APPEND aqm_CCTM_files
 	${MECHS}/RXNS_DATA_MODULE.F90
 	${MECHS}/RXNS_FUNC_MODULE.F90
 	${PA}/PA_DEFN.F
+        ${PA}/budget_defn.F
+        ${PA}/../../hadv/ppm/xy_budget.F
 	${PA}/pa_update.F
+        ${PA}/PA_IRR_module.F
+        ${PA}/PA_IRR_CTL.F
 	${PHOT}/CLOUD_OPTICS.F
 	${PHOT}/complex_number_module.F90
 	${PHOT}/CSQY_DATA.F
-	${PHOT}/OMI_1979_to_2015.dat
+	${PHOT}/OMI_1979_to_2019.dat
 	${PHOT}/opphot.F
-	${PHOT}/phot.F
 	${PHOT}/PHOT_MET_DATA.F
 	${PHOT}/PHOT_MOD.F
 	${PHOT}/PHOTOLYSIS_ALBEDO.F
 	${PHOT}/PHOT_OPTICS.dat
 	${PHOT}/SEAS_STRAT_O3_MIN.F
 	${PHOT}/twoway_rrtmg_aero_optics.F90
+        ${PHOT}/concld_prop_acm.F
 	${PLRISE}/delta_zs.f
 	${PLRISE}/fire_plmris.F
 	${PLRISE}/openlayout.F
 	${PLRISE}/oppt3d_diag.F
 	${PLRISE}/plmris.F
 	${PLRISE}/plsprd.f
 	${PLRISE}/preplm.f
-	${PLRISE}/ungridb2.f
 	${PLRISE}/write3_distr.f
 	${SPCS}/CGRID_SPCS.F
+        ${SPCS}/CGRID_SPCS_TYPES.F
+        ${STM}/STM_VARS.F
+        ${STM}/STM_MODULE.F
 	${STENEX}/noop_comm_module.f
 	${STENEX}/noop_data_copy_module.f
 	${STENEX}/noop_gather_module.f
@@ -215,32 +231,45 @@ list(APPEND aqm_CCTM_files
 	${STENEX}/noop_slice_module.f
 	${STENEX}/noop_term_module.f
 	${STENEX}/noop_util_module.f
-	${UTIL}/bmatvec.F
 	${UTIL}/findex.f
-	${UTIL}/get_envlist.f
+        ${UTIL}/log_header.F
+	#${UTIL}/get_env_mod.f90
 	${UTIL}/setup_logdev.F
 	${UTIL}/subhdomain.F
 	${UTIL}/UTILIO_DEFN.F
+        #${UTIL}/RUNTIME_VARS.F
+        ${UTIL}/util_family_module.F
+	#${UTIL}/CMAQ_Control_Misc.nml
+        ${DRIV}/ELMO_PROC.F
+        ${DRIV}/ELMO_DATA.F
 	${VDIFF}/aero_sedv.F
+        ${VDIFF}/aero_depv.F
 	${VDIFF}/conv_cgrid.F
 	${VDIFF}/matrix1.F
 	${VDIFF}/opddep.F
-	${VDIFF}/opddep_fst.F
-	${VDIFF}/opddep_mos.F
-	${VDIFF}/rddepv.F
 	${VDIFF}/SEDIMENTATION.F
 	${VDIFF}/tri.F
+        ${VDIFF}/VDIFF_DATA.F
 	${VDIFF}/VDIFF_DIAG.F
 	${VDIFF}/VDIFF_MAP.F
 	${VDIFF}/vdiffproc.F
+        #${CIO}/centralized_io_module.F
 	${localCCTM}/o3totcol.f
-	${localCCTM}/vdiffacmx.F
-	${localCCTM}/PTMAP.F
-	${localCCTM}/PT3D_DATA_MOD.F
+	#${localCCTM}/AERO_EMIS.F
+        #${localCCTM}/PTMAP.F
+	#${localCCTM}/PT3D_DATA_MOD.F
+	#rbdriver.F has a typo in CMAQ.Put it back to {GAS} if they solve it in the future
+	${localCCTM}/rbdriver.F
 	${localCCTM}/PT3D_DEFN.F
 	${localCCTM}/PT3D_FIRE_DEFN.F
 	${localCCTM}/PT3D_STKS_DEFN.F
+        ${localCCTM}/vdiffacmx.F
 	${localCCTM}/ASX_DATA_MOD.F
 	${localCCTM}/DUST_EMIS.F
 	${localCCTM}/AERO_PHOTDATA.F
+	${localCCTM}/phot.F
+        ${localCCTM}/RUNTIME_VARS.F
+        ${localCCTM}/get_env_mod.f90
+        ${localCCTM}/centralized_io_module.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

@@ -13,7 +13,8 @@ module AQM
   implicit none
 
   ! -- import fields
-  integer, parameter :: importFieldCount = 36
+  integer, parameter :: importFieldCount = 37
+!  integer, parameter :: importFieldCount = 45  !with canopy
   character(len=*), dimension(importFieldCount), parameter :: &
     importFieldNames = (/ &
       "canopy_moisture_storage                  ", &
@@ -51,7 +52,8 @@ module AQM
       "soil_type                                ", &
       "surface_cell_area                        ", &
       "surface_snow_area_fraction               ", &
-      "temperature_of_soil_layer                "  &
+      "temperature_of_soil_layer                ", &
+      "vegetation_type                          " &
     /)
   ! -- export fields
   integer, parameter :: exportFieldCount = 2