Add GOCART DMS process

CMakeLists.txt

@@ -45,5 +45,6 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel" AND CMAKE_BUILD_TYPE MATCHES "D
     6379,10448)
 endif()
 
+add_subdirectory(util)
 add_subdirectory(src)
 add_subdirectory(tests)

src/api/CMakeLists.txt

@@ -8,5 +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(${_lib} PUBLIC CATChem_process_suvolcanic)
+target_link_libraries(${_lib} PUBLIC CATChem_process_DMS)
 set_target_properties(${_lib} PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
 target_compile_options(${_lib} PRIVATE ${_catchem_compiler_options})

src/api/catchem.F90

@@ -82,6 +82,16 @@ module CATChem
    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
+   ! SUVolcanicEmissions
+   use CCPr_SUVolcanicEmissions_mod, only: SUVolcanicEmissionsStateType                            !< SUVolcanicEmissions State
+   use CCPr_SUVolcanicEmissions_mod, only: cc_suvolcanic_init => CCPr_SUVolcanicEmissions_Init         !< SUVolcanicEmissions Process Initialization Routine
+   use CCPr_SUVolcanicEmissions_mod, only: cc_suvolcanic_run => CCPr_SUVolcanicEmissions_Run           !< SUVolcanicEmissions Process Run Routine
+   use CCPr_SUVolcanicEmissions_mod, only: cc_suvolcanic_finalize => CCPr_SUVolcanicEmissions_Finalize !< SUVolcanicEmissions Process Finalization Routine
+   ! DMS
+   use CCPr_DMS_mod, only: DMSStateType                         !< DMS State
+   use CCPr_DMS_mod, only: cc_dms_init => CCPr_DMS_Init         !< DMS Process Initialization Routine
+   use CCPr_DMS_mod, only: cc_dms_run => CCPr_DMS_Run           !< DMS Process Run Routine
+   use CCPr_DMS_mod, only: cc_dms_finalize => CCPr_DMS_Finalize !< DMS Process Finalization Routine
 
    implicit none
 

src/core/chemstate_mod.F90

@@ -40,12 +40,14 @@ module ChemState_Mod
    !! \param nSpeciesGas: The number of gas species.
    !! \param nSpeciesAero: The number of aerosol species.
    !! \param nSpeciesDust: The number of dust species.
-   !! \param nSpeicesSeaSalt: The number of sea salt species.
+   !! \param nSpeciesSeaSalt: The number of sea salt species.
    !! \param SpeciesIndex: An array containing the total species index.
    !! \param AeroIndex: An array containing the aerosol species index.
    !! \param GasIndex: An array containing the gas species index.
    !! \param DustIndex: An array containing the dust species index.
+   !! \param DryDepIndex: An array containing the dry deposition species index.
    !! \param SeaSaltIndex: An array containing the sea salt species index.
+   !! \param SUVolcanicIndex: An array containing the Sulfur volcanic species index.
    !! \param chemSpecies: A 2-D array containing the concentration of each species.
    !!
    !! \ingroup core_modules
@@ -66,13 +68,15 @@ module ChemState_Mod
       INTEGER              :: nSpeciesTracer    !< Number of Tracer Species
       INTEGER              :: nSpeciesDust      !< Number of Dust Species
       INTEGER              :: nSpeciesSeaSalt   !< Number of SeaSalt Species
+      INTEGER              :: nSpeciesSUVolcanic !< Number of Volcanic Sulfur Species
       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
+      INTEGER, ALLOCATABLE :: SUVolcanicIndex(:)   !< Volcanic sulfur Species Index
       CHARACTER(len=50), ALLOCATABLE :: SpeciesNames(:)  !< Species Names
 
       !---------------------------------------------------------------------
@@ -183,6 +187,7 @@ subroutine Find_Number_of_Species(ChemState, RC)
       ChemState%nSpeciesGas = 0
       ChemState%nSpeciesSeaSalt = 0
       ChemState%nSpeciesTracer = 0
+      ChemState%nSpeciesSUVolcanic = 0
 
       ! Count number of species
       do i = 1, ChemState%nSpecies
@@ -204,6 +209,9 @@ subroutine Find_Number_of_Species(ChemState, RC)
          if (ChemState%ChemSpecies(i)%is_drydep .eqv. .true.) then
             ChemState%nSpeciesAeroDryDep = ChemState%nSpeciesAeroDryDep + 1
          endif
+         if (ChemState%ChemSpecies(i)%is_suvolcanic .eqv. .true.) then
+            ChemState%nSpeciesSUVolcanic = ChemState%nSpeciesSUVolcanic + 1
+         endif
       enddo
 
    end subroutine Find_Number_of_Species
@@ -238,6 +246,7 @@ subroutine Find_Index_of_Species(ChemState, RC)
       integer :: seasalt_index   ! Current Seas Salt Index
       integer :: tracer_index    ! Current Tracer Index
       integer :: drydep_index    ! Current DryDep Index
+      integer :: suvolcanic_index    ! Current SUVolcanic Index
 
 
       ! Initialize
@@ -253,6 +262,7 @@ subroutine Find_Index_of_Species(ChemState, RC)
       seasalt_index = 1
       tracer_index = 1
       drydep_index = 1
+      suvolcanic_index = 1
 
       ! Allocate index arrays
       ALLOCATE(Chemstate%AeroIndex(ChemState%nSpeciesAero), STAT=RC)
@@ -297,6 +307,13 @@ subroutine Find_Index_of_Species(ChemState, RC)
          RETURN
       ENDIF
 
+      ALLOCATE(Chemstate%SUVolcanicIndex(ChemState%nSpeciesSUVolcanic), STAT=RC)
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error allocating Chemstate%SUVolcanicIndex'
+         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
@@ -323,6 +340,10 @@ subroutine Find_Index_of_Species(ChemState, RC)
             Chemstate%DryDepIndex(drydep_index) = n
             drydep_index = drydep_index + 1
          endif
+         if (ChemState%ChemSpecies(n)%is_suvolcanic .eqv. .true.) then
+            Chemstate%SUVolcanicIndex(suvolcanic_index) = n
+            suvolcanic_index = suvolcanic_index + 1
+         endif
       enddo
 
    end subroutine Find_index_of_Species

src/core/config_mod.F90

@@ -173,6 +173,24 @@ SUBROUTINE Read_Input_File( Config , GridState, EmisState, ChemState, RC, Config
          RETURN
       ENDIF
 
+      call Config_Process_DMS(ConfigInput, Config, RC)
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error in "Config_Process_DMS"!'
+         CALL CC_Error( errMsg, RC, thisLoc  )
+         CALL QFYAML_CleanUp( ConfigInput         )
+         CALL QFYAML_CleanUp( ConfigAnchored )
+         RETURN
+      ENDIF
+
+      call Config_Process_SUVolcanicEmissions(ConfigInput, Config, RC)
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error in "Config_Process_SUVolcanicEmissions"!'
+         CALL CC_Error( errMsg, RC, thisLoc  )
+         CALL QFYAML_CleanUp( ConfigInput         )
+         CALL QFYAML_CleanUp( ConfigAnchored )
+         RETURN
+      ENDIF
+
 
       !========================================================================
       ! Config ChemState
@@ -236,7 +254,7 @@ SUBROUTINE Config_Chem_State( filename, GridState, ChemState, RC )
       real    :: v_real
       logical :: v_logical
 
-      Character(len=17) :: tags(17)
+      Character(len=17) :: tags(19)
 
       RC = CC_SUCCESS
 
@@ -255,6 +273,8 @@ SUBROUTINE Config_Chem_State( filename, GridState, ChemState, RC )
          'is_gas           ', &
          'is_advected      ', &
          'is_photolysis    ', &
+         'is_suvolcanic    ', &
+         'is_dms           ', &
          'mw_g             ', &
          'viscosity        ', &
          'density          ', &
@@ -403,6 +423,26 @@ SUBROUTINE Config_Chem_State( filename, GridState, ChemState, RC )
          ChemState%ChemSpecies(n)%is_drydep = v_logical
          write(*,*) '|  is_drydep: ', ChemState%ChemSpecies(n)%is_drydep
 
+         key = TRIM(ChemState%SpeciesNames(n)) // '%' // 'is_suvolcanic'
+         v_logical = MISSING_BOOL
+         CALL QFYAML_Add_Get( ConfigInput, TRIM(key), v_logical, "", RC )
+         IF (RC /= CC_SUCCESS) then
+            ! assume that if is_suvolcanic isn't in the species.yaml file assume false
+            ChemState%ChemSpecies(n)%is_suvolcanic = MISSING_BOOL
+         ENDIF
+         ChemState%ChemSpecies(n)%is_suvolcanic = v_logical
+         write(*,*) '|  is_suvolcanic: ', ChemState%ChemSpecies(n)%is_suvolcanic
+
+         key = TRIM(ChemState%SpeciesNames(n)) // '%' // 'is_dms'
+         v_logical = MISSING_BOOL
+         CALL QFYAML_Add_Get( ConfigInput, TRIM(key), v_logical, "", RC )
+         IF (RC /= CC_SUCCESS) then
+            ! assume that if is_dms isn't in the species.yaml file assume false
+            ChemState%ChemSpecies(n)%is_dms = MISSING_BOOL
+         ENDIF
+         ChemState%ChemSpecies(n)%is_dms = v_logical
+         write(*,*) '|  is_dms: ', ChemState%ChemSpecies(n)%is_dms
+
          key = TRIM(ChemState%SpeciesNames(n)) // '%' // 'is_photolysis'
          v_logical = MISSING_BOOL
          CALL QFYAML_Add_Get( ConfigInput, TRIM(key), v_logical, "", RC )
@@ -569,6 +609,8 @@ SUBROUTINE Config_Chem_State( filename, GridState, ChemState, RC )
       write(*,*) '|  number of tracers:  ', ChemState%nSpeciesTracer
       write(*,*) '|  number of dust:     ', ChemState%nSpeciesDust
       write(*,*) '|  number of seasalt:  ', ChemState%nSpeciesSeaSalt
+      write(*,*) '|  number of volcanic:  ', ChemState%nSpeciesSUVolcanic
+
       write(*,*) '========================================================='
 
    END SUBROUTINE Config_Chem_State
@@ -1179,7 +1221,7 @@ SUBROUTINE Config_Process_SeaSalt( ConfigInput, Config, RC )
       RC      = CC_SUCCESS
       thisLoc = ' -> at Config_Process_SeaSalt (in CATChem/src/core/config_mod.F90)'
       errMsg = ''
-      
+
       key   = "process%seasalt%activate"
       v_bool = MISSING_BOOL
       CALL QFYAML_Add_Get( ConfigInput, TRIM( key ), v_bool, "", RC )
@@ -1373,4 +1415,154 @@ SUBROUTINE Config_Process_DryDep( ConfigInput, Config, RC )
    END SUBROUTINE Config_Process_DryDep
 
 
+   !> \brief Process SUVolcanicEmissions configuration
+   !!
+   !! This function processes the SUVolcanic 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_SUVolcanicEmissions( 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
+
+      ! Strings
+      CHARACTER(LEN=255)           :: thisLoc
+      CHARACTER(LEN=512)           :: errMsg
+      CHARACTER(LEN=QFYAML_StrLen) :: key
+
+      !========================================================================
+      ! Config_Process_SUVolcanicEmissions begins here!
+      !========================================================================
+
+      ! Initialize
+      RC      = CC_SUCCESS
+      thisLoc = ' -> at Config_Process_SUVolcanicEmissions (in CATChem/src/core/config_mod.F90)'
+      errMsg = ''
+
+      ! TODO #105 Fix reading of config file
+      key   = "process%SUVolcanicEmissions%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%SUVolcanicEmissions%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%SUVolcanicEmissions_scheme = v_int
+
+
+      write(*,*) "SUVolcanicEmissions Configuration"
+      write(*,*) '------------------------------------'
+      write(*,*) 'Config%SUVolcanicEmissions_activate = ', Config%SUVolcanicEmissions_activate
+      write(*,*) 'Config%SUVolcanicEmissions_scheme = ', Config%SUVolcanicEmissions_scheme
+      write(*,*) '------------------------------------'
+
+   END SUBROUTINE Config_Process_SUVolcanicEmissions
+
+
+   !> \brief Process DMS configuration
+   !!
+   !! This function processes the DMS 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_DMS( 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
+
+      ! Strings
+      CHARACTER(LEN=255)           :: thisLoc
+      CHARACTER(LEN=512)           :: errMsg
+      CHARACTER(LEN=QFYAML_StrLen) :: key
+
+      !========================================================================
+      ! Config_Process_DMS begins here!
+      !========================================================================
+
+      ! Initialize
+      RC      = CC_SUCCESS
+      thisLoc = ' -> at Config_Process_DMS (in CATChem/src/core/config_mod.F90)'
+      errMsg = ''
+
+      ! TODO #105 Fix reading of config file
+      key   = "process%DMS%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%DMS_activate = v_bool
+
+
+      key   = "process%DMS%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%DMS_scheme = v_int
+
+      write(*,*) "DMS Configuration"
+      write(*,*) '------------------------------------'
+      write(*,*) 'Config%DMS_activate = ', Config%DMS_activate
+      write(*,*) 'Config%DMS_scheme = ', Config%DMS_scheme
+      write(*,*) '------------------------------------'
+
+
+   END SUBROUTINE Config_Process_DMS
+
+
 END MODULE config_mod