Add Wesely and Zhang dry dep schemes

.codespellrc

@@ -1,2 +1,2 @@
 [codespell]
-ignore-words-list = inout,iland
+ignore-words-list = inout,iland,thik

.github/workflows/ci.yml

@@ -37,7 +37,7 @@ jobs:
 
       - name: Build
         run: |
-          cmake -B $BUILD_DIR
+          cmake -B $BUILD_DIR -DCMAKE_POLICY_VERSION_MINIMUM=3.5
           cmake --build $BUILD_DIR
         env:
           FC: ${{ matrix.compiler }}

src/api/CMakeLists.txt

@@ -8,6 +8,7 @@ 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)
+target_link_libraries(${_lib} PUBLIC CATChem_process_bvoc)
 target_link_libraries(${_lib} PUBLIC CATChem_process_chem)
 set_target_properties(
   ${_lib}

src/api/catchem.F90

@@ -85,6 +85,13 @@ module CATChem
    ! Chemical mechanism solver
    use CCPr_Chem_mod, only: cc_get_micm_version => get_micm_version
 
+   ! BVOC emissions
+   use CCPr_Bvoc_Common_Mod, only: BvocStateType                             !< BVOC State
+   use CCPr_Bvoc_mod, only: cc_bvoc_init => CCPr_Bvoc_Init                   !< BVOC Process Initialization Routine
+   use CCPr_Bvoc_mod, only: cc_bvoc_run => CCPr_Bvoc_Run                     !< BVOC Process Run Routine
+   use CCPr_Bvoc_mod, only: cc_bvoc_finalize => CCPr_Bvoc_Final              !< BVOC Process Finalization Routine
+
+
    implicit none
 
    public

src/core/chemstate_mod.F90

@@ -22,6 +22,7 @@ module ChemState_Mod
    PUBLIC :: Chem_Allocate
    PUBLIC :: Find_Number_of_Species
    PUBLIC :: Find_Index_of_Species
+   PUBLIC :: Find_SeaSalt_Bin
    PUBLIC :: FindSpecByName
    PUBLIC :: GetSpecConc
    PUBLIC :: GetSpecConcByName
@@ -63,16 +64,21 @@ module ChemState_Mod
       INTEGER              :: nSpeciesGas       !< Number of Gas Species
       INTEGER              :: nSpeciesAero      !< Number of Aerosol Species
       INTEGER              :: nSpeciesAeroDryDep !< Number of Aerosol Species for Dry Dep
+      INTEGER              :: nSpeciesDryDep     !< Number of all Species for Dry Dep
       INTEGER              :: nSpeciesTracer    !< Number of Tracer Species
       INTEGER              :: nSpeciesDust      !< Number of Dust Species
       INTEGER              :: nSpeciesSeaSalt   !< Number of SeaSalt Species
+      INTEGER              :: nSpeciesBin       !< Number of SeaSalt Species Bin
       INTEGER, ALLOCATABLE :: SpeciesIndex(:)   !< Total Species Index
       INTEGER, ALLOCATABLE :: TracerIndex(:)    !< Tracer Species Index
       INTEGER, ALLOCATABLE :: AeroIndex(:)      !< Aerosol Species Index
       INTEGER, ALLOCATABLE :: GasIndex(:)       !< Gas Species Index
       INTEGER, ALLOCATABLE :: DustIndex(:)      !< Dust Species Index
       INTEGER, ALLOCATABLE :: SeaSaltIndex(:)   !< SeaSalt Species Index
-      INTEGER, ALLOCATABLE :: DryDepIndex(:)   !< SeaSalt Species Index
+      real(fp),ALLOCATABLE :: SeaSaltBinLower(:)  !< SeaSalt Species Bin Lower edge
+      real(fp),ALLOCATABLE :: SeaSaltBinUpper(:) !< SeaSalt Species Bin upper edge
+      INTEGER, ALLOCATABLE :: AeroDryDepIndex(:) !< Aerosol DryDep Species Index for Dry Dep
+      INTEGER, ALLOCATABLE :: DryDepIndex(:)   !< All DryDep Species Index
       CHARACTER(len=50), ALLOCATABLE :: SpeciesNames(:)  !< Species Names
 
       !---------------------------------------------------------------------
@@ -179,6 +185,7 @@ subroutine Find_Number_of_Species(ChemState, RC)
       ! Initialize to zero before counting species
       ChemState%nSpeciesAero = 0
       ChemState%nSpeciesAeroDryDep = 0
+      ChemState%nSpeciesDryDep = 0
       ChemState%nSpeciesDust = 0
       ChemState%nSpeciesGas = 0
       ChemState%nSpeciesSeaSalt = 0
@@ -201,9 +208,13 @@ 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
+         if ( (ChemState%ChemSpecies(i)%is_drydep .eqv. .true.) .and. &
+            (ChemState%ChemSpecies(i)%is_aerosol .eqv. .true.)   ) then
             ChemState%nSpeciesAeroDryDep = ChemState%nSpeciesAeroDryDep + 1
          endif
+         if (ChemState%ChemSpecies(i)%is_drydep .eqv. .true.) then
+            ChemState%nSpeciesDryDep = ChemState%nSpeciesDryDep + 1
+         endif
       enddo
 
    end subroutine Find_Number_of_Species
@@ -237,6 +248,7 @@ 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 :: aero_drydep_index ! Current Aerosol DryDep Index
       integer :: drydep_index    ! Current DryDep Index
 
 
@@ -252,6 +264,7 @@ subroutine Find_Index_of_Species(ChemState, RC)
       dust_index = 1
       seasalt_index = 1
       tracer_index = 1
+      aero_drydep_index = 1
       drydep_index = 1
 
       ! Allocate index arrays
@@ -290,7 +303,14 @@ subroutine Find_Index_of_Species(ChemState, RC)
          RETURN
       ENDIF
 
-      ALLOCATE(Chemstate%DryDepIndex(ChemState%nSpeciesAeroDryDep), STAT=RC)
+      ALLOCATE(Chemstate%AeroDryDepIndex(ChemState%nSpeciesAeroDryDep), STAT=RC)
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error allocating Chemstate%AeroDryDepIndex'
+         call CC_Error(errMsg, RC, thisLoc)
+         RETURN
+      ENDIF
+
+      ALLOCATE(Chemstate%DryDepIndex(ChemState%nSpeciesDryDep), STAT=RC)
       IF ( RC /= CC_SUCCESS ) THEN
          errMsg = 'Error allocating Chemstate%DryDepIndex'
          call CC_Error(errMsg, RC, thisLoc)
@@ -319,6 +339,11 @@ 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.) .and. &
+            (ChemState%ChemSpecies(n)%is_aerosol .eqv. .true.)    ) then
+            Chemstate%AeroDryDepIndex(aero_drydep_index) = n
+            aero_drydep_index = aero_drydep_index + 1
+         endif
          if (ChemState%ChemSpecies(n)%is_drydep .eqv. .true.) then
             Chemstate%DryDepIndex(drydep_index) = n
             drydep_index = drydep_index + 1
@@ -327,6 +352,101 @@ subroutine Find_Index_of_Species(ChemState, RC)
 
    end subroutine Find_index_of_Species
 
+   !> \brief Find the bins of sea salt species
+   !!
+   !! \param ChemState The ChemState object
+   !! \param RC The return code
+   !!
+   !! \ingroup core_modules
+   !!!>
+   subroutine Find_SeaSalt_Bin(ChemState, RC)
+      ! USES
+      !USE Species_Mod,  ONLY : SpeciesType
+
+      IMPLICIT NONE
+
+      ! INOUT Params
+      type(ChemStateType),  INTENT(INOUT) :: ChemState     ! chem State object
+      ! OUTPUT Params
+      INTEGER,             INTENT(OUT)   :: RC            ! Success or failure
+
+      ! Error handling
+      CHARACTER(LEN=255) :: ErrMsg
+      CHARACTER(LEN=255) :: thisLoc
+
+      ! Local variables
+      integer   :: n                  ! looping variable
+      integer   :: n_bin              ! number of sea salt bins
+      !real(fp)  :: radius0           ! initial radius of sea salt bin
+      real(fp)  :: lower_radius(10)   ! lower radius of sea salt bin holder
+      real(fp)  :: upper_radius(10)   ! upper radius of sea salt bin holder
+      logical   :: mask(10) = .FALSE. ! flag to for sorting bins by radius
+
+      ! Initialize
+      RC = CC_SUCCESS
+      ErrMsg = ''
+      thisLoc = ' -> at Find_SeaSalt_Bin (in core/chemstate_mod.F90)'
+
+
+      ! Initialize to zero before counting species
+      n_bin = 0
+      !radius0 = 0.0_fp
+
+      ! Find possible sea salt bins
+      do n = 1, ChemState%nSpeciesSeaSalt
+         if (n == 1) then
+            n_bin = 1
+            lower_radius(n_bin) = ChemState%ChemSpecies(Chemstate%SeaSaltIndex(n))%lower_radius
+            upper_radius(n_bin) = ChemState%ChemSpecies(Chemstate%SeaSaltIndex(n))%upper_radius
+         else
+            if (  ALL( ABS(lower_radius(1:n_bin) - ChemState%ChemSpecies(Chemstate%SeaSaltIndex(n))%lower_radius) > 0.0_fp )) then
+               n_bin = n_bin + 1
+               lower_radius(n_bin) = ChemState%ChemSpecies(Chemstate%SeaSaltIndex(n))%lower_radius
+               upper_radius(n_bin) = ChemState%ChemSpecies(Chemstate%SeaSaltIndex(n))%upper_radius
+            endif
+         endif
+      enddo
+
+      ! Allocate index arrays
+      ALLOCATE(Chemstate%SeaSaltBinLower(n_bin), STAT=RC)
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error allocating Chemstate%SeaSaltBinLower'
+         call CC_Error(errMsg, RC, thisLoc)
+         RETURN
+      ENDIF
+
+      ALLOCATE(Chemstate%SeaSaltBinUpper(n_bin), STAT=RC)
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error allocating Chemstate%SeaSaltBinUpper'
+         call CC_Error(errMsg, RC, thisLoc)
+         RETURN
+      ENDIF
+
+      !sort bins by radius from low to high for lower_radius
+      mask(1:n_bin) = .TRUE.
+      do n = 1, n_bin
+         Chemstate%SeaSaltBinLower(n) =  MINVAL(lower_radius,mask)
+         mask(MINLOC(lower_radius,mask)) = .FALSE.
+      enddo
+
+      !sort bins by radius from low to high for upper_radius
+      mask(1:n_bin) = .TRUE.
+      do n = 1, n_bin
+         Chemstate%SeaSaltBinUpper(n) =  MINVAL(upper_radius,mask)
+         mask(MINLOC(upper_radius,mask)) = .FALSE.
+      enddo
+
+      !check if the bins are continuous
+      do n = 1, n_bin-1
+         if ( .not. rae(Chemstate%SeaSaltBinUpper(n), Chemstate%SeaSaltBinLower(n+1)) ) then
+            errMsg = 'Sea Salt Bins are not continuous'
+            call CC_Error(errMsg, RC, thisLoc)
+            RETURN
+         endif
+      enddo
+
+   end subroutine Find_SeaSalt_Bin
+
    !> \brief Find the species by name
    !!
    !! \param ChemState The ChemState object