updates to dry dep, incl. test

src/CMakeLists.txt

@@ -1,4 +1,4 @@
 add_subdirectory(core)
-add_subdirectory(process)
 add_subdirectory(external)
+add_subdirectory(process)
 add_subdirectory(api)

src/api/CMakeLists.txt

@@ -7,5 +7,6 @@ target_link_libraries(${_lib} PUBLIC CATChem_core)
 target_link_libraries(${_lib} PUBLIC CATChem_process_dust)
 target_link_libraries(${_lib} PUBLIC CATChem_process_seasalt)
 target_link_libraries(${_lib} PUBLIC CATChem_process_plumerise)
+target_link_libraries(${_lib} PUBLIC CATChem_process_drydep)
 set_target_properties(${_lib} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
 target_compile_options(${_lib} PRIVATE ${_catchem_compiler_options})

src/api/catchem.F90

@@ -77,6 +77,11 @@ module CATChem
    use CCPr_Plumerise_mod, only: cc_plumerise_init => CCPr_Plumerise_Init         !< Plumerise Process Initialization Routine
    use CCPr_Plumerise_mod, only: cc_plumerise_run => CCPr_Plumerise_Run           !< Plumerise Process Run Routine
    use CCPr_Plumerise_mod, only: cc_plumerise_finalize => CCPr_Plumerise_Finalize !< Plumerise Process Finalization Routine
+   ! Dry Dep
+   use CCPr_DryDep_mod, only: DryDepStateType                               !< DryDep State
+   use CCPr_DryDep_mod, only: cc_drydep_init => CCPr_DryDep_Init         !< DryDep Process Initialization Routine
+   use CCPr_DryDep_mod, only: cc_drydep_run => CCPr_DryDep_Run           !< DryDep Process Run Routine
+   use CCPr_DryDep_mod, only: cc_drydep_finalize => CCPr_DryDep_Finalize !< DryDep Process Finalization Routine
 
    implicit none
 

src/core/chemstate_mod.F90

@@ -1,5 +1,4 @@
-!>
-!! \file chemstate_mod.F90
+!> \file chemstate_mod.F90
 !! \brief Contains the `ChemStateType` data type and related subroutines and functions.
 !!
 !!
@@ -63,6 +62,7 @@ module ChemState_Mod
       INTEGER              :: nSpecies          !< Total Number of Species
       INTEGER              :: nSpeciesGas       !< Number of Gas Species
       INTEGER              :: nSpeciesAero      !< Number of Aerosol Species
+      INTEGER              :: nSpeciesAeroDryDep !< Number of Aerosol Species for Dry Dep
       INTEGER              :: nSpeciesTracer    !< Number of Tracer Species
       INTEGER              :: nSpeciesDust      !< Number of Dust Species
       INTEGER              :: nSpeciesSeaSalt   !< Number of SeaSalt Species
@@ -72,6 +72,7 @@ module ChemState_Mod
       INTEGER, ALLOCATABLE :: GasIndex(:)       !< Gas Species Index
       INTEGER, ALLOCATABLE :: DustIndex(:)      !< Dust Species Index
       INTEGER, ALLOCATABLE :: SeaSaltIndex(:)   !< SeaSalt Species Index
+      INTEGER, ALLOCATABLE :: DryDepIndex(:)   !< SeaSalt Species Index
       CHARACTER(len=50), ALLOCATABLE :: SpeciesNames(:)  !< Species Names
 
       !---------------------------------------------------------------------
@@ -100,11 +101,13 @@ subroutine Chem_Allocate(GridState, ChemState, RC)
       ! USES
       USE GridState_Mod,  ONLY : GridStateType
       USE Species_Mod,    Only : SpeciesType
+      USE Metstate_Mod
 
       IMPLICIT NONE
 
       ! INOUT Params
       type(GridStateType), INTENT(in)    :: GridState ! Grid State object
+      !type(MetStateType), INTENT(in)    :: MetState   ! Met State object
       type(ChemStateType), INTENT(inout) :: ChemState ! chem State object
       ! type(SpeciesType),   POINTER       :: Species   ! Species object
       ! OUTPUT Params
@@ -176,6 +179,7 @@ subroutine Find_Number_of_Species(ChemState, RC)
 
       ! Initialize to zero before counting species
       ChemState%nSpeciesAero = 0
+      ChemState%nSpeciesAeroDryDep = 0
       ChemState%nSpeciesDust = 0
       ChemState%nSpeciesGas = 0
       ChemState%nSpeciesSeaSalt = 0
@@ -198,6 +202,9 @@ subroutine Find_Number_of_Species(ChemState, RC)
          if (ChemState%ChemSpecies(i)%is_tracer .eqv. .true.) then
             ChemState%nSpeciesTracer = ChemState%nSpeciesTracer + 1
          endif
+         if (ChemState%ChemSpecies(i)%is_drydep .eqv. .true.) then
+            ChemState%nSpeciesAeroDryDep = ChemState%nSpeciesAeroDryDep + 1
+         endif
       enddo
 
    end subroutine Find_Number_of_Species
@@ -231,6 +238,7 @@ subroutine Find_Index_of_Species(ChemState, RC)
       integer :: dust_index      ! Current Dust Index
       integer :: seasalt_index   ! Current Seas Salt Index
       integer :: tracer_index    ! Current Tracer Index
+      integer :: drydep_index    ! Current DryDep Index
 
 
       ! Initialize
@@ -245,6 +253,7 @@ subroutine Find_Index_of_Species(ChemState, RC)
       dust_index = 1
       seasalt_index = 1
       tracer_index = 1
+      drydep_index = 1
 
       ! Allocate index arrays
       ALLOCATE(Chemstate%AeroIndex(ChemState%nSpeciesAero), STAT=RC)
@@ -282,6 +291,13 @@ subroutine Find_Index_of_Species(ChemState, RC)
          RETURN
       ENDIF
 
+      ALLOCATE(Chemstate%DryDepIndex(ChemState%nSpeciesAeroDryDep), STAT=RC)
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error allocating Chemstate%DryDepIndex'
+         call CC_Error(errMsg, RC, thisLoc)
+         RETURN
+      ENDIF
+
       ! Find indices for species groups
       do n = 1, ChemState%nSpecies
          if (ChemState%ChemSpecies(n)%is_aerosol .eqv. .true.) then
@@ -304,6 +320,10 @@ subroutine Find_Index_of_Species(ChemState, RC)
             Chemstate%TracerIndex(tracer_index) = n
             tracer_index = tracer_index + 1
          endif
+         if (ChemState%ChemSpecies(n)%is_drydep .eqv. .true.) then
+            Chemstate%DryDepIndex(drydep_index) = n
+            drydep_index = drydep_index + 1
+         endif
       enddo
 
    end subroutine Find_index_of_Species

src/core/config_mod.F90

@@ -94,7 +94,7 @@ SUBROUTINE Read_Input_File( Config , GridState, EmisState, ChemState, RC, Config
       ! Assume success
       RC      = CC_SUCCESS
       errMsg  = ''
-      thisLoc = ' -> at Read_Input_File (in module CATChem/src/core/input_mod.F90)'
+      thisLoc = ' -> at Read_Input_File (in module CATChem/src/core/config_mod.F90)'
 
       !========================================================================
       ! Read the YAML file into the Config object
@@ -164,6 +164,16 @@ SUBROUTINE Read_Input_File( Config , GridState, EmisState, ChemState, RC, Config
          RETURN
       ENDIF
 
+      call Config_Process_DryDep(ConfigInput, Config, RC)
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error in "Config_Process_DryDep"!'
+         CALL CC_Error( errMsg, RC, thisLoc  )
+         CALL QFYAML_CleanUp( ConfigInput         )
+         CALL QFYAML_CleanUp( ConfigAnchored )
+         RETURN
+      ENDIF
+
+
       !========================================================================
       ! Config ChemState
       !========================================================================
@@ -554,6 +564,7 @@ SUBROUTINE Config_Chem_State( filename, GridState, ChemState, RC )
       write(*,*) '| Chemstate SUMMARY'
       write(*,*) '|  number_of_species:  ', ChemState%nSpecies
       write(*,*) '|  number_of_aerosols: ', ChemState%nSpeciesAero
+      write(*,*) '|  number_of_aerosols with dry dep: ', ChemState%nSpeciesAeroDryDep
       write(*,*) '|  number_of_gases:    ', ChemState%nSpeciesGas
       write(*,*) '|  number of tracers:  ', ChemState%nSpeciesTracer
       write(*,*) '|  number of dust:     ', ChemState%nSpeciesDust
@@ -1256,7 +1267,7 @@ SUBROUTINE Config_Process_Plumerise( ConfigInput, Config, RC )
 
       ! Initialize
       RC      = CC_SUCCESS
-      thisLoc = ' -> at Config_Process_SeaSalt (in CATChem/src/core/config_mod.F90)'
+      thisLoc = ' -> at Config_Process_Plumerise (in CATChem/src/core/config_mod.F90)'
       errMsg = ''
 
       key   = "process%plumerise%activate"
@@ -1276,4 +1287,103 @@ SUBROUTINE Config_Process_Plumerise( ConfigInput, Config, RC )
 
    END SUBROUTINE Config_Process_Plumerise
 
+
+   !> \brief Process DryDep configuration
+   !!
+   !! This function processes the DryDep configuration and performs the necessary actions based on the configuration.
+   !!
+   !! \param[in] ConfigInput The YAML configuration object
+   !! \param[inout] Config The configuration object
+   !! \param[out] RC The return code
+   !!
+   !! \ingroup core_modules
+   !!!>
+   SUBROUTINE Config_Process_DryDep( ConfigInput, Config, RC )
+      USE CharPak_Mod,    ONLY : StrSplit
+      USE Error_Mod
+      USE Config_Opt_Mod,  ONLY : ConfigType
+
+      TYPE(QFYAML_t),      INTENT(INOUT) :: ConfigInput      ! YAML Config object
+      TYPE(ConfigType),     INTENT(INOUT) :: Config   ! Input options
+
+      !
+      ! !OUTPUT PARAMETERS:
+      !
+      INTEGER,        INTENT(OUT)   :: RC          ! Success or failure
+      ! !LOCAL VARIABLES:
+      !
+      ! Scalars
+      LOGICAL                      :: v_bool
+      INTEGER                      :: v_int
+      INTEGER                      :: nSubStrs
+      INTEGER                      :: N
+      INTEGER                      :: C
+
+      ! Reals
+      REAL(fp)                     :: v_real
+
+      ! Arrays
+      INTEGER                      :: a_int(4)
+
+      ! Strings
+      CHARACTER(LEN=255)           :: thisLoc
+      CHARACTER(LEN=512)           :: errMsg
+      CHARACTER(LEN=QFYAML_StrLen) :: key
+      CHARACTER(LEN=QFYAML_StrLen) :: v_str
+
+      ! String arrays
+      CHARACTER(LEN=255)           :: subStrs(MAXDIM)
+      CHARACTER(LEN=QFYAML_StrLen) :: a_str(2)
+
+      !========================================================================
+      ! Config_Process_DryDep begins here!
+      !========================================================================
+
+      ! Initialize
+      RC      = CC_SUCCESS
+      thisLoc = ' -> at Config_Process_DryDep (in CATChem/src/core/config_mod.F90)'
+      errMsg = ''
+
+      ! TODO #105 Fix reading of config file
+      key   = "process%drydep%activate"
+      v_bool = MISSING_BOOL
+      CALL QFYAML_Add_Get( ConfigInput, TRIM( key ), v_bool, "", RC )
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error parsing ' // TRIM( key ) // '!'
+         CALL CC_Error( errMsg, RC, thisLoc )
+         RETURN
+      ENDIF
+      Config%drydep_activate = v_bool
+
+
+      key   = "process%drydep%scheme_opt"
+      v_int = MISSING_INT
+      CALL QFYAML_Add_Get( ConfigInput, TRIM( key ), v_int, "", RC )
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = TRIM( key ) // 'Not Found, Setting Default to 1'
+         v_int = 1 ! default is one
+         RETURN
+      ENDIF
+      Config%drydep_scheme = v_int
+
+
+      key   = "process%drydep%resuspension"
+      v_bool = MISSING_BOOL
+      CALL QFYAML_Add_Get( ConfigInput, TRIM( key ), v_bool, "", RC )
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = TRIM( key ) // 'Not Found, Setting Default to FALSE'
+         RETURN
+      ENDIF
+      Config%drydep_resuspension = v_bool
+
+      write(*,*) "DryDeposition Configuration"
+      write(*,*) '------------------------------------'
+      write(*,*) 'Config%drydep_activate = ', Config%drydep_activate
+      write(*,*) 'Config%drydep_scheme = ', Config%drydep_scheme
+      write(*,*) 'Config%drydep_resuspension = ', Config%drydep_resuspension
+      write(*,*) '------------------------------------'
+
+   END SUBROUTINE Config_Process_DryDep
+
+
 END MODULE config_mod

src/core/config_opt_mod.F90

@@ -42,6 +42,9 @@ MODULE Config_Opt_Mod
    !! - `dust_scheme_opt` : Scheme option for dust process
    !! - `seasalt_activate` : Activate seasalt process
    !! - `seasalt_scheme_opt` : Scheme option for seasalt process
+   !! - `drydep_activate` : Activate drydep process
+   !! - `drydep_scheme` : Scheme option for drydep process
+   !! - `drydep_resuspension` : Activate resuspension
    !!
    !! \ingroup core_modules
    !!!>
@@ -94,7 +97,10 @@ MODULE Config_Opt_Mod
       ! Plumerise Process
       LOGICAL                     :: plumerise_activate
 
-
+      ! DryDeposition Process
+      LOGICAL                     :: drydep_activate
+      INTEGER                     :: drydep_scheme
+      LOGICAL                     :: drydep_resuspension  ! Turn on resuspension
 
    END TYPE ConfigType
 
@@ -165,7 +171,10 @@ SUBROUTINE Set_Config( am_I_Root, Config, RC )
       Config%seasalt_activate = .FALSE.
       Config%seasalt_scheme = 1
 
-
+      ! Dry Dep Process
+      Config%drydep_activate = .FALSE.
+      Config%drydep_scheme = 1
+      Config%drydep_resuspension = .FALSE.
 
    END SUBROUTINE Set_Config
    !> \brief Cleanup the Config options

src/core/diagstate_mod.F90

@@ -22,6 +22,14 @@ module DiagState_Mod
    !!
    !! \ingroup core_modules
    !!
+   !! \param dust_total_flux      Total flux of dust particles [kg m-2 s-1]
+   !! \param sea_salt_total_flux  Total flux of sea salt particles [kg m-2 s-1]
+   !! \param AOD550               Total AOD at 550nm [1]
+   !! \param AOD380               Total AOD at 380nm [1]
+   !! \param TOMSAI               TOMS Aerosol Index [1]
+   !! \param briggs_plumerise_height Effective plume rise height from Briggs algorithm [m]
+   !! \param sofiev_plumerise_height Effective plume rise height from Sofiev algorithm [m]
+   !!
    !!!>
    type, public :: DiagStateType
 
@@ -39,6 +47,10 @@ module DiagState_Mod
       real(fp) :: briggs_plumerise_height !< Effective plume rise height from Briggs algorithm [m]
       real(fp) :: sofiev_plumerise_height !< Effective plume rise height from Sofiev algorithm [m]
 
+
+      real(fp), allocatable :: drydep_frequency(:)
+      real(fp), allocatable :: drydep_vel(:)
+
       ! Species Specific Variables
 
 
@@ -56,15 +68,16 @@ module DiagState_Mod
    !! \param RC The return code
    !! \ingroup core_modules
    !!!>
-   subroutine Diag_Allocate(Config, DiagState, RC)
+   subroutine Diag_Allocate(Config, DiagState, ChemState, RC)
       ! USES
-      USE GridState_Mod, ONLY : GridStateType
+      ! USE GridState_Mod, ONLY : GridStateType
       USE Config_Opt_Mod, ONLY : ConfigType
 
       ! Arguments
       type(ConfigType),    INTENT(IN)    :: Config
       ! type(GridStateType), INTENT(IN)    :: GridState ! Grid State object
       type(DiagStateType), INTENT(INOUT) :: DiagState ! Diag State object
+      type(ChemStateType), INTENT(INOUT) :: ChemState ! Chem State object
       ! OUTPUT Params
       INTEGER,             INTENT(OUT)   :: RC        ! Success or failure
 
@@ -91,6 +104,26 @@ subroutine Diag_Allocate(Config, DiagState, RC)
          DiagState%sea_salt_total_flux = ZERO
       endif
 
+      ! If dry deposition process is activated then allocate dry dep related diagnostics
+      if (Config%drydep_activate) then
+         Allocate(diagstate%drydep_frequency(ChemState%nSpeciesAeroDryDep), STAT=RC)
+         IF ( RC /= CC_SUCCESS ) THEN
+            ErrMsg = 'Could not Allocate ChemState%ChemSpecies(i)%conc'
+            CALL CC_Error( ErrMsg, RC, thisLoc )
+         ENDIF
+         DiagState%drydep_frequency= ZERO
+         Allocate(diagstate%drydep_vel(ChemState%nSpeciesAeroDryDep), STAT=RC)
+         IF ( RC /= CC_SUCCESS ) THEN
+            ErrMsg = 'Could not Allocate ChemState%ChemSpecies(i)%conc'
+            CALL CC_Error( ErrMsg, RC, thisLoc )
+         ENDIF
+         DiagState%drydep_vel= ZERO
+
+
+      endif
+
+
+
    end subroutine Diag_Allocate
 
 end module DiagState_Mod

src/core/emisstate_mod.F90

@@ -159,13 +159,13 @@ subroutine Emis_Allocate(GridState, EmisState, RC)
       integer :: s ! Loop counter for emitted species
       ! integer :: nPlumes ! temporary variable for number of plumes
 
-
       ! Initialize return code
       RC = CC_SUCCESS
 
       ! Initialize local variables
       ErrMsg = ''
       ThisLoc = ' -> at Emis_Allocate (in core/emisstate_mod.F90)'
+
       if (EmisState%nCats > 0) then
          print*, 'Number of Categories = ', EmisState%nCats
          do c = 1, EmisState%nCats
@@ -384,7 +384,6 @@ subroutine Apply_Emis_to_Chem(EmisState, MetState, ChemState, RC, surface_only_f
       TYPE(MetStateType),  INTENT(IN)    :: MetState
       TYPE(ChemStateType), INTENT(INOUT) :: ChemState
       LOGICAL, INTENT(IN), OPTIONAL :: surface_only_flag
-
       INTEGER, INTENT(OUT) :: RC
 
       ! Local