Merge branch 'develop' into tclune-patch-1

CHANGELOG.md

@@ -14,9 +14,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - Modified the file paths in carbon, sulfate, and nitrate ExtData.yaml files to used the revised version of the CEDS anthropogenic emissions. Note the previous version has an incorrect seasonal cycle.
-- Sulfate surface area density calculation in SU_Compute_Diags was incorrectly being passed the effective radius used for settling along with the sigma width of the number distribution. Properly it should be passed the number median radius, also present in the RC file. Added a hook to read that field from the RC file ("particle_radius_number"), store in SU grid comp, and pass to SU_Compute_Diags. This change is zero-diff to the SU internal state. It changes value of export SO4AREA.
-- Changed DMS concentration data holder from ExtData provided (SU_DMSO) to local copy (dmso_conc). This is relevant since if we run source tagged instances where we don't want DMS emissions we would zero out dmso_conc and that is what should be passed to DMSemission subroutine. This is zero diff except in that case.
+- Sulfate surface area density calculation in SU_Compute_Diags was incorrectly being passed the effective radius used for settling along with the sigma width of the number distribution. 
+  Properly it should be passed the number median radius, also present in the RC file. Added a hook to read that field from the RC file ("particle_radius_number"), store in SU grid comp, and pass to SU_Compute_Diags. 
+  This change is zero-diff to the SU internal state. It changes value of export SO4AREA.
+- Changed DMS concentration data holder from ExtData provided (SU_DMSO) to local copy (dmso_conc). 
+  This is relevant since if we run source tagged instances where we don't want DMS emissions we would zero out dmso_conc and that is what should be passed to DMSemission subroutine. This is zero diff except in that case.
 - Changed SU2G_instance_SU.rc to now have separate filename inputs for explosive and degassing volcanoes
+- It changes the formulation of the hydrophobic to hydrophilic conversion for carbon species, now defined by a time scale specified in the instance RC file.
+  This is now specified by providing an e-folding time in days. This moves the time constant from outside the fortran to the run-time configurable RC file. 
+  This is not quite zero-diff with original code because of the precision of the specification, but testing shows nearly zero-diff result.
+- Also now present in the carbon instance RC files is a run-time configurable optional parameterized loss rate (e-folding time in days) per species and per mode. 
+  Default value for all is set to "-1" which means no use of this function.
 
 ### Fixed
 
@@ -28,12 +36,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Corrected the units of the gravimetric soil moisture to percent instead of fractional in the FENGSHA dust scheme.
 - Fix issue of GOCART/GEOSgcm circular CMake dependencies when used as external project
 - Fix UFS/Standalone CMake issue
+- Fix type of `k` in `SUvolcanicEmissions`
 
 ### Added
 
 - Additional tuning parameters for the soil moisture and drylimit calculations for application specific tuning.
-- Required attributes for the 2D GOCART export fields in AERO_DP bundle have been set in subroutine append_to_bundle in Chem_AeroGeneric.F90. These export fields are imported by OBIO via Surface GC, and the missing of the attributes was causing the writing of surface import checkpoint to fail. The issue has been explained in detail on https://github.com/GEOS-ESM/GOCART/issues/258
-
+- Required attributes for the 2D GOCART export fields in AERO_DP bundle have been set in subroutine append_to_bundle in Chem_AeroGeneric.F90. 
+  These export fields are imported by OBIO via Surface GC, and the missing of the attributes was causing the writing of surface import checkpoint to fail. 
+  The issue has been explained in detail on https://github.com/GEOS-ESM/GOCART/issues/258
 - Added export line to GOCART2G_GridCompMod to couple allow use of GOCART
   SU sulfate production tendency elsewhere in Chemistry, specifically for
   CARMA
@@ -49,9 +59,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   until an actual split is made in the input emissions then the volcanic emissions are being assigned to
   one or the other emission diagnostics (explosive or degassing).
 
-- Changed Chem_SettlingSimple in the process library to call Mie Query for radius and rhop inputs to the settling velocity calculation. The calls to Chem_SettlingSimple were then changed accordingly in each of the species' grid comps. Since the RH flag is no longer needed, it was removed from GA_EnvironmentMod.F90 and each of the instance RC files.
+- Changed Chem_SettlingSimple in the process library to call Mie Query for radius and rhop inputs to the settling velocity calculation. 
+  The calls to Chem_SettlingSimple were then changed accordingly in each of the species' grid comps. 
+  Since the RH flag is no longer needed, it was removed from GA_EnvironmentMod.F90 and each of the instance RC files.
 - State Spec RC files for GOCART2G, CA, DU, NI, SU, and SS were updated such that the long names for AOD are more intuitive
-- Modified ExtData.yaml files to persist as climatological anthropogenic emissions after the end of the CEDS dataset in 2019. Analogous rc files removed as this capability is only available with ExtData2G
+- Modified ExtData.yaml files to persist as climatological anthropogenic emissions after the end of the CEDS dataset in 2019. 
+  Analogous rc files removed as this capability is only available with ExtData2G
 - Update `components.yaml` to match that of GEOSgcm v11.6.1
   - ESMA_env v4.29.0 (Baselibs 7.24.0, Updates for SLES15 at NCCS, various fixes)
   - ESMA_cmake v3.48.0 (Fixes for NAS, debug flags, Updates for SLES15 at NCCS, MPI detection, ESMF and MPI CMake fixes for Spack)

ESMF/GOCART2G_GridComp/CA2G_GridComp/CA2G_GridCompMod.F90

@@ -55,6 +55,8 @@ module CA2G_GridCompMod
        real               :: fMonoterpenes = 0.0 ! Fraction of monoterpene emissions -> aerosol
        real               :: fIsoprene = 0.0 ! Franction of isoprene emissions -> aerosol
        real               :: fHydrophobic ! Initially hydrophobic portion
+       real               :: tConvPhobicToPhilic ! e-folding time [days] hydrophobic to hydrophilic
+       real               :: tChemLoss(2)        ! e-folding time [days] for parameterized chemistry loss
        logical            :: diurnal_bb   ! diurnal biomass burning
        real               :: eAircraftfuel       ! Aircraft emission factor: go from kg fuel to kg C
        real               :: aviation_layers(4)  ! heights of the LTO, CDS and CRS layers
@@ -163,6 +165,12 @@ subroutine SetServices (GC, RC)
 !   ----------------------------------------------
     call ESMF_ConfigGetAttribute (cfg, self%myDOW, label='my_day_of_week:', default=-1, __RC__)
     call ESMF_ConfigGetAttribute (cfg, self%fhydrophobic, label='hydrophobic_fraction:', __RC__)
+    call ESMF_ConfigGetAttribute (cfg, self%tConvPhobicToPhilic, &
+                                  label='time_days_hydrophobic_to_hydrophilic:', default=2.5, __RC__)
+    call ESMF_ConfigFindLabel (cfg, 'time_days_chemical_destruction:', __RC__)
+    do i=1,size(self%tChemLoss)
+     call ESMF_ConfigGetAttribute (cfg, self%tChemLoss(i), default=-1., __RC__)
+    end do
     call ESMF_ConfigGetAttribute (cfg, self%ratPOM, label='pom_ca_ratio:', default=1.0, __RC__)
     call ESMF_ConfigGetAttribute (cfg, self%fMonoterpenes, label='monoterpenes_emission_fraction:', default=0.0, __RC__)
     call ESMF_ConfigGetAttribute (cfg, self%fIsoprene, label='isoprene_emission_fraction:', default=0.0, __RC__)
@@ -998,9 +1006,20 @@ subroutine Run2 (GC, import, export, clock, RC)
     end if
 
 !   Ad Hoc transfer of hydrophobic to hydrophilic aerosols
-!   Following Chin's parameterization, the rate constant is
-!   k = 4.63e-6 s-1 (.4 day-1; e-folding time = 2.5 days)
-    call phobicTophilic (intPtr_phobic, intPtr_philic, HYPHIL, self%km, self%cdt, MAPL_GRAV, delp, __RC__)
+!   Rate controlled in RC file; tConvPhobicToPhilic < 0 means no transfer
+    call phobicToPhilic (intPtr_phobic, intPtr_philic, HYPHIL, &
+                         self%tConvPhobicToPhilic, self%km, self%cdt, MAPL_GRAV, delp, __RC__)
+
+!   Ad Hoc chemical destruction of carbon
+!   This applies a simple exponential decay to both hydrophobic and
+!   hydrophilic modes with the time constant tChemLoss (e-folding
+!   time in days)
+    do n = 1, self%nbins
+       call MAPL_VarSpecGet(InternalSpec(n), SHORT_NAME=short_name, __RC__)
+       call MAPL_GetPointer(internal, NAME=short_name, ptr=int_ptr, __RC__)
+       call carbonChemLoss (self%km, self%klid, n, self%cdt, MAPL_GRAV, delp, &
+                            self%tChemLoss(n), int_ptr, CH, __RC__)
+    end do
 
 !   CA Settling
 !   -----------

ESMF/GOCART2G_GridComp/CA2G_GridComp/CA2G_StateSpecs.rc

@@ -89,6 +89,7 @@ category: EXPORT
  *DP          | kg m-2 s-1   | xy    | N     | nbins                          | * Aerosol Dry Deposition (Bin %d)
  *WT          | kg m-2 s-1   | xy    | N     | nbins                          | * Aerosol Wet Deposition (Bin %d)
  *SV          | kg m-2 s-1   | xy    | N     | nbins                          | * Aerosol Convective Scavenging (Bin %d)
+ *CH          | kg m-2 s-1   | xy    | N     | nbins                          | * Aerosol Parameterized Chemical Loss (Bin %d)
  *EMAN        | kg m-2 s-1   | xy    | N     |                                | * Aerosol Anthropogenic Emissions
  *EMBB        | kg m-2 s-1   | xy    | N     |                                | * Aerosol Biomass Burning Emissions
  *EMBF        | kg m-2 s-1   | xy    | N     |                                | * Aerosol Biofuel Emissions

ESMF/GOCART2G_GridComp/CA2G_GridComp/CA2G_instance_CA.bc.rc

@@ -14,6 +14,12 @@ aviation_vertical_layers: 0.0 100.0 9.0e3 10.0e3
 # Initially hydrophobic portion
 hydrophobic_fraction: 0.8
 
+# Rate of conversion of hydrophobic to hydrophilic [days]
+time_days_hydrophobic_to_hydrophilic: 2.5
+
+# Rate of chemical destruction of carbon species [days]
+time_days_chemical_destruction: -1.  -1.
+
 # Scavenging efficiency per bin [km-1] (NOT USED UNLESS RAS IS CALLED)
 fscav: 0.0  0.4 
 

ESMF/GOCART2G_GridComp/CA2G_GridComp/CA2G_instance_CA.br.rc

@@ -20,6 +20,12 @@ particle_radius_microns: 0.35 0.35
 # Initially hydrophobic portion
 hydrophobic_fraction: 0.5
 
+# Rate of conversion of hydrophobic to hydrophilic [days]
+time_days_hydrophobic_to_hydrophilic: 2.5
+
+# Rate of chemical destruction of carbon species [days]
+time_days_chemical_destruction: -1.   -1.
+
 # Scavenging efficiency per bin [km-1] (NOT USED UNLESS RAS IS CALLED)
 fscav: 0.0  0.4 
 

ESMF/GOCART2G_GridComp/CA2G_GridComp/CA2G_instance_CA.oc.rc

@@ -24,6 +24,12 @@ particle_radius_microns: 0.35 0.35
 # Initially hydrophobic portion
 hydrophobic_fraction: 0.5
 
+# Rate of conversion of hydrophobic to hydrophilic [days]
+time_days_hydrophobic_to_hydrophilic: 2.5
+
+# Rate of chemical destruction of carbon species [days]
+time_days_chemical_destruction: -1.  -1.
+
 # Scavenging efficiency per bin [km-1] (NOT USED UNLESS RAS IS CALLED)
 fscav: 0.0  0.4 
 

Process_Library/GOCART2G_Process.F90

@@ -41,7 +41,8 @@ module  GOCART2G_Process
    public wetRadius
    public hoppelCorrection
    public CAEmission
-   public phobicTophilic
+   public phobicToPhilic
+   public carbonChemLoss
    public NIheterogenousChem
    public SulfateDistributeEmissions
    public DMSemission
@@ -4682,16 +4683,17 @@ end subroutine distribute_aviation_emissions
 
 !BOP
 !
-! !IROUTINE: phobicTophilic
+! !IROUTINE: phobicToPhilic
 !
 ! !INTERFACE:
    subroutine phobicTophilic (aerosol_phobic, aerosol_philic, aerosol_toHydrophilic, &
-                              km, cdt, grav, delp, rc)
+                              tConvPhobicToPhilic, km, cdt, grav, delp, rc)
 
 ! !USES:
    implicit NONE
 
 ! !INPUT PARAMETERS:
+   real, intent(in)      :: tConvPhobicToPhilic  ! e-folding time in days to transfer
    integer, intent(in)   :: km   ! total model level
    real, intent(in)      :: cdt  ! chemistry model time-step [sec]
    real, intent(in)      :: grav ! [m/sec^2]
@@ -4706,18 +4708,25 @@ subroutine phobicTophilic (aerosol_phobic, aerosol_philic, aerosol_toHydrophilic
 
 ! !Local Variables
    integer :: i, j, k
-   real :: qUpdate, delq
+   real :: qUpdate, delq, ts
 
 !EOP
 !------------------------------------------------------------------------------------
 !  Begin...
 
    if(associated(aerosol_toHydrophilic)) aerosol_toHydrophilic = 0.0
 
+!  tConvPhobicToPhilic is the e-folding time (in days) of the conversion
+!  If < 0 no conversion is desired; exit the subroutine
+   if(tConvPhobicToPhilic < 0) then
+    __RETURN__(__SUCCESS__)
+   endif
+   ts = tConvPhobicToPhilic*86400.
+
    do k = 1, km
     do j = 1, ubound(delp, 2)
      do i = 1, ubound(delp, 1)
-      qUpdate = aerosol_phobic(i,j,k)*exp(-4.63e-6*cdt)
+      qUpdate = aerosol_phobic(i,j,k)*exp(-cdt/ts)
       qUpdate = max(qUpdate,1.e-32)
       delq = max(0.,aerosol_phobic(i,j,k)-qUpdate)
       aerosol_phobic(i,j,k) = qUpdate
@@ -4732,6 +4741,70 @@ subroutine phobicTophilic (aerosol_phobic, aerosol_philic, aerosol_toHydrophilic
    __RETURN__(__SUCCESS__)
   end subroutine phobicTophilic
 
+!============================================================================
+!BOP
+!
+! !IROUTINE: carbonChemLoss
+!
+! !INTERFACE:
+   subroutine carbonChemLoss (km, klid, n, cdt, grav, delp, &
+                              tChemLoss, int_qa, fluxout, rc)
+
+! !USES:
+   implicit NONE
+
+! !INPUT PARAMETERS:
+   real, intent(in)       :: tChemLoss  ! e-folding loss time [days]
+   integer, intent(in)    :: km         ! total model levels
+   integer, intent(in)    :: klid       ! index for pressure lid
+   integer, intent(in)    :: n          ! bin index number
+   real, intent(in)       :: cdt        ! time step [s]
+   real, intent(in)       :: grav       ! acceleration of gravity [m/sec^2]
+   real, dimension(:,:,:), intent(inout)          :: int_qa  ! aerosol [kg/kg]
+   real, pointer, dimension(:,:,:), intent(in)    :: delp    ! pressure level thickness [Pa]
+
+! !OUTPUT PARAMETERS:
+
+   real, pointer, dimension(:,:,:), intent(inout) :: fluxout ! Mass lost by chemistry [kg/m^2/s]
+   integer, optional, intent(out)                 :: rc      ! Error return code:
+                                                             !  0 - all is well
+                                                             !  1 -
+
+! !Local Variables
+   integer :: i, j, k
+   real :: qUpdate, delq, ts
+
+!EOP
+!------------------------------------------------------------------------------------
+!  Begin...
+
+   if(associated(fluxout)) fluxout(:,:,n) = 0.0
+
+!  tChemLoss is the e-folding time (in days) of parameterized chemistry loss
+!  If < 0 no loss is desired; exit the subroutine
+   if(tChemLoss < 0) then
+    __RETURN__(__SUCCESS__)
+   endif
+   ts = tChemLoss*86400.
+
+   do k = klid, km
+    do j = 1, ubound(delp, 2)
+     do i = 1, ubound(delp, 1)
+      qUpdate = int_qa(i,j,k)*exp(-cdt/ts)
+      qUpdate = max(qUpdate,1.e-32)
+      delq = max(0.,int_qa(i,j,k)-qUpdate)
+      int_qa(i,j,k) = qUpdate
+      if(associated(fluxout)) &
+       fluxout(i,j,n) = fluxout(i,j,n) &
+        + delq*delp(i,j,k)/grav/cdt
+
+     end do
+    end do
+   end do
+
+   __RETURN__(__SUCCESS__)
+  end subroutine carbonChemLoss
+
 
 !============================================================================
 !BOP
@@ -5703,11 +5776,11 @@ subroutine SUvolcanicEmissions (nVolc, vStart, vEnd, vSO2, vElev, vCloud, iPoint
 ! 22July2020 E.Sherman
 !
 ! !Local Variables
-   integer  ::  i, j, it
+   integer  ::  i, j, k, it
    real, dimension(:,:,:), allocatable  :: emissions_point
    real :: so2volcano
 
-   real :: hup, hlow, dzvolc, dz, z1, k
+   real :: hup, hlow, dzvolc, dz, z1
    real :: deltaSO2v
    real, dimension(:,:), allocatable :: z0
    real, allocatable, dimension(:,:) :: srcSO2volc