Add GOCART DMS process

src/api/CMakeLists.txt

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

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_Volcanic_mod, only: VolcanicStateType                                         !< SUVolcanic State
+   use CCPr_Volcanic_mod, only: cc_volcanic_init => CCPr_Volcanic_Init         !< SUVolcanicEmissions Process Initialization Routine
+   use CCPr_Volcanic_mod, only: cc_volcanic_run => CCPr_Volcanic_Run           !< SUVolcanicEmissions Process Run Routine
+   use CCPr_Volcanic_mod, only: cc_volcanic_finalize => CCPr_Volcanic_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
    ! Chemical mechanism solver
    use CCPr_Chem_mod, only: cc_get_micm_version => get_micm_version
 

src/core/chemstate_mod.F90

@@ -40,13 +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 SeaSaltIndex: An array containing the sea salt species index.
-   !! \param chemSpecies: A 2-D array containing the concentration of each species.
+   !! \param DryDepIndex: An array containing the dry deposition species index.
+   !! \param SpeciesNames: A character array containing the names of the species.
    !!
    !! \ingroup core_modules
    !!!>
@@ -362,6 +363,11 @@ subroutine FindSpecByName(ChemState, name, index, RC)
             exit
          endif
       enddo
+      if (index == 0) then
+         RC = CC_FAILURE
+         ErrMsg = 'Species not found: ' // TRIM(name)
+         call CC_Warning(ErrMsg, RC, thisLoc)
+      endif
 
    end subroutine FindSpecByName
 

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_Volcanic(ConfigInput, Config, RC)
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error in "Config_Process_Volcanic"!'
+         CALL CC_Error( errMsg, RC, thisLoc  )
+         CALL QFYAML_CleanUp( ConfigInput         )
+         CALL QFYAML_CleanUp( ConfigAnchored )
+         RETURN
+      ENDIF
+
 
       !========================================================================
       ! Config ChemState
@@ -1373,4 +1391,165 @@ SUBROUTINE Config_Process_DryDep( ConfigInput, Config, RC )
    END SUBROUTINE Config_Process_DryDep
 
 
+   !> \brief Process Volcanic configuration
+   !!
+   !! This function processes the Volcanic 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_Volcanic( 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
+      CHARACTER(LEN=1055)           :: v_str
+
+      ! Strings
+      CHARACTER(LEN=255)           :: thisLoc
+      CHARACTER(LEN=512)           :: errMsg
+      CHARACTER(LEN=QFYAML_StrLen) :: key
+
+      !========================================================================
+      ! Config_Process_Volcanic begins here!
+      !========================================================================
+
+      ! Initialize
+      RC      = CC_SUCCESS
+      thisLoc = ' -> at Config_Process_Volcanic (in CATChem/src/core/config_mod.F90)'
+      errMsg = ''
+
+      ! TODO #105 Fix reading of config file
+      key   = "process%volcanic%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%volcanic_activate = v_bool
+
+
+      key   = "process%volcanic%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%volcanic_scheme = v_int
+
+      key   = "process%volcanic%filedir"
+      v_str = MISSING_STR
+      CALL QFYAML_Add_Get( ConfigInput, TRIM( key ), v_str, "", RC )
+      IF ( RC /= CC_SUCCESS ) THEN
+         errMsg = 'Error parsing ' // TRIM( key ) // '!'
+         CALL CC_Warning( errMsg, RC, thisLoc )
+      ENDIF
+      Config%volcanic_filedir = TRIM( v_str )
+
+
+      write(*,*) "Volcanic Configuration"
+      write(*,*) '------------------------------------'
+      write(*,*) 'Config%volcanic_activate = ', Config%volcanic_activate
+      write(*,*) 'Config%volcanic_scheme = ', Config%volcanic_scheme
+      write(*,*) 'Config%volcanic_filedir = ', Config%volcanic_filedir
+      write(*,*) '------------------------------------'
+
+   END SUBROUTINE Config_Process_Volcanic
+
+
+   !> \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

src/core/config_opt_mod.F90

@@ -45,6 +45,11 @@ MODULE Config_Opt_Mod
    !! - `drydep_activate` : Activate drydep process
    !! - `drydep_scheme` : Scheme option for drydep process
    !! - `drydep_resuspension` : Activate resuspension
+   !! - `volcanic_activate` : Activate Volcanic process
+   !! - `volcanic_scheme` : Scheme option for Volcanic process
+   !! - `volcanic_filedir` : File directory for Volcanic process
+   !! - `DMS_activate` : Activate DMS emissions
+   !! - `DMS_scheme` : Scheme option DMS process
    !!
    !! \ingroup core_modules
    !!!>
@@ -102,6 +107,15 @@ MODULE Config_Opt_Mod
       INTEGER                     :: drydep_scheme
       LOGICAL                     :: drydep_resuspension  !< Turn on resuspension
 
+      ! VolcanicEmissions Process
+      LOGICAL                     :: volcanic_activate
+      INTEGER                     :: volcanic_scheme
+      character(len=1055)         :: volcanic_filedir
+
+      ! DMS Process
+      LOGICAL                     :: DMS_activate
+      INTEGER                     :: DMS_scheme
+
    END TYPE ConfigType
 
 CONTAINS
@@ -176,6 +190,15 @@ SUBROUTINE Set_Config( am_I_Root, Config, RC )
       Config%drydep_scheme = 1
       Config%drydep_resuspension = .FALSE.
 
+      ! SU Volcanic Process
+      Config%volcanic_activate = .FALSE.
+      Config%volcanic_scheme = 1
+      Config%volcanic_filedir = ' '
+
+      ! DMS Process
+      Config%DMS_activate = .FALSE.
+      Config%DMS_scheme = 1
+
    END SUBROUTINE Set_Config
    !> \brief Cleanup the Config options
    !!

src/core/emisstate_mod.F90

@@ -358,7 +358,6 @@ subroutine Emis_Find_Chem_Map_Index(EmisState, ChemState, RC)
                   return
                endif
                EmisState%Cats(c)%Species(s)%EmisMapIndex(n) = index
-               EmisState%Cats(c)%Species(s)%EmisMapIndex(n) = index
             enddo
          enddo
       enddo

src/core/metstate_mod.F90

@@ -45,6 +45,8 @@ MODULE MetState_Mod
       ! TIMESTEP
       !---------
       REAL(fp)              :: TSTEP             !< Time step [s]
+      INTEGER               :: YMD              ! Year, month, day
+      INTEGER               :: HMS              ! Hour, minute, second
 
       ! Logicals
       !---------
@@ -192,6 +194,9 @@ MODULE MetState_Mod
       REAL(fp), ALLOCATABLE :: PMID(:)        !< Average wet air pressure [hPa] defined as arithmetic average of edge pressures
       REAL(fp), ALLOCATABLE :: PMID_DRY(:)    !< Dry air partial pressure [hPa] defined as arithmetic avg of edge pressures
 
+      !TODO: temporary put DMS concentration here for DMS emissions from gocart; may read from ChemState in the future
+      REAL(fp)              :: DMSO_CONC      !< DMS concentration [mol/L]
+
    END TYPE MetStateType
 
 CONTAINS

src/core/qfyaml_mod.F90

@@ -1159,15 +1159,9 @@ SUBROUTINE QFYAML_Read_Emis_File( yml, fileName, yml_anchored, EmisState, RC )
                      cspecies = TRIM(yml%vars(n)%category(ix+1:))
                      tmpString = TRIM(yml%vars(n)%category(ix+1:))
                      names = [names, tmpString]
+                     j = j + 1 ! increment species index
                   endif
                endif
-
-               if ((n == yml%num_vars) .and. (TRIM(yml%vars(n)%category(1:ix-1)) == TRIM(current))) then
-                  cspecies = TRIM(yml%vars(n)%category(ix+1:))
-                  tmpString = TRIM(yml%vars(n)%category(ix+1:))
-                  names = [names, tmpString]
-                  j = j + 1
-               endif
             enddo
 
             ! Fill last category species names

src/process/CMakeLists.txt

@@ -4,4 +4,6 @@ add_subdirectory(dust)
 add_subdirectory(seasalt)
 add_subdirectory(plumerise)
 add_subdirectory(drydep)
+add_subdirectory(dms)
+add_subdirectory(volcanic)
 add_subdirectory(chem)