Add scm_zero_non_iop_tracers option.

components/eam/bld/namelist_files/namelist_definition.xml

@@ -4095,6 +4095,13 @@ Default: FALSE
        group="cam_inparm" valid_values="">
 Turn off microphysics computation.
 Default: FALSE
+</entry>                                                                        |
+                                                                                |
+<entry id="scm_zero_non_iop_tracers" type="logical" category="scam"
+       group="cam_inparm" valid_values="">
+Ignore all tracers from initial conditions file, and default all tracers not
+specified in IOP to minimum value (usually zero).
+Default: FALSE
 </entry>
 
 <!-- Solar Parameters -->

components/eam/src/control/runtime_opts.F90

@@ -174,6 +174,7 @@ module runtime_opts
 logical  :: scm_crm_mode
 logical  :: scm_observed_aero
 logical  :: precip_off
+logical  :: scm_zero_non_iop_tracers
 
 contains
 
@@ -324,7 +325,8 @@ subroutine read_namelist(single_column_in, scmlon_in, scmlat_in, nlfilename_in )
    namelist /cam_inparm/ iopfile,scm_iop_srf_prop,scm_relaxation, &
                          scm_relaxation_low, scm_relaxation_high, &
                          scm_diurnal_avg,scm_crm_mode,scm_clubb_iop_name, &
-                         scm_observed_aero, precip_off
+                         scm_observed_aero, precip_off, &
+                         scm_zero_non_iop_tracers
 
 !-----------------------------------------------------------------------
 
@@ -369,7 +371,8 @@ subroutine read_namelist(single_column_in, scmlon_in, scmlat_in, nlfilename_in )
         scm_crm_mode_out=scm_crm_mode, &
         scm_observed_aero_out=scm_observed_aero, &
         precip_off_out=precip_off, &
-        scm_clubb_iop_name_out=scm_clubb_iop_name)
+        scm_clubb_iop_name_out=scm_clubb_iop_name, &
+        scm_zero_non_iop_tracers_out=scm_zero_non_iop_tracers)
    end if
 
    ! Read in the cam_inparm namelist from input filename
@@ -446,7 +449,8 @@ subroutine read_namelist(single_column_in, scmlon_in, scmlat_in, nlfilename_in )
                             scm_crm_mode_in=scm_crm_mode, &
                             scm_observed_aero_in=scm_observed_aero, &
                             precip_off_in=precip_off, &
-                            scm_clubb_iop_name_in=scm_clubb_iop_name)
+                            scm_clubb_iop_name_in=scm_clubb_iop_name, &
+                            scm_zero_non_iop_tracers_in=scm_zero_non_iop_tracers)
       end if
    endif
 

components/eam/src/control/scamMod.F90

@@ -184,6 +184,7 @@ module scamMod
   logical*4, public ::  scm_relaxation! use relaxation
   logical*4, public ::  scm_observed_aero ! use observed aerosols in SCM file
   logical*4, public ::  precip_off    ! turn off precipitation processes
+  logical*4, public ::  scm_zero_non_iop_tracers ! initialize non-IOP-specified tracers to zero
   logical*4, public ::  use_replay    ! use e3sm generated forcing 
   logical*4, public ::  use_3dfrc     ! use 3d forcing
   logical*4, public ::  have_heat_glob ! dataset contains global energy fixer
@@ -203,7 +204,7 @@ subroutine scam_default_opts( scmlat_out,scmlon_out,iopfile_out, &
         single_column_out,scm_iop_srf_prop_out, scm_relaxation_out, &
         scm_relaxation_low_out, scm_relaxation_high_out, &
         scm_diurnal_avg_out, scm_crm_mode_out, scm_observed_aero_out, &
-        precip_off_out, scm_clubb_iop_name_out)
+        precip_off_out, scm_clubb_iop_name_out, scm_zero_non_iop_tracers_out)
 !-----------------------------------------------------------------------
    real(r8), intent(out), optional :: scmlat_out,scmlon_out
    character*(max_path_len), intent(out), optional ::  iopfile_out
@@ -217,6 +218,7 @@ subroutine scam_default_opts( scmlat_out,scmlon_out,iopfile_out, &
    real(r8), intent(out), optional ::  scm_relaxation_low_out
    real(r8), intent(out), optional ::  scm_relaxation_high_out   
    character(len=*), intent(out), optional ::  scm_clubb_iop_name_out
+   logical, intent(out), optional ::  scm_zero_non_iop_tracers_out
 
    if ( present(scmlat_out) )           scmlat_out     = -999._r8
    if ( present(scmlon_out) )           scmlon_out     = -999._r8
@@ -231,14 +233,16 @@ subroutine scam_default_opts( scmlat_out,scmlon_out,iopfile_out, &
    if ( present(scm_observed_aero_out)) scm_observed_aero_out = .false.
    if ( present(precip_off_out))        precip_off_out = .false.
    if ( present(scm_clubb_iop_name_out) ) scm_clubb_iop_name_out  = ' '
+   if ( present(scm_zero_non_iop_tracers_out) ) scm_zero_non_iop_tracers_out = .false.
 
 end subroutine scam_default_opts
 
 subroutine scam_setopts( scmlat_in, scmlon_in,iopfile_in,single_column_in, &
                          scm_iop_srf_prop_in, scm_relaxation_in, &
                          scm_relaxation_low_in, scm_relaxation_high_in, &
                          scm_diurnal_avg_in, scm_crm_mode_in, scm_observed_aero_in, &
-                         precip_off_in, scm_clubb_iop_name_in)
+                         precip_off_in, scm_clubb_iop_name_in, &
+                         scm_zero_non_iop_tracers_in)
 !-----------------------------------------------------------------------
   real(r8), intent(in), optional       :: scmlon_in, scmlat_in
   character*(max_path_len), intent(in), optional :: iopfile_in
@@ -252,6 +256,7 @@ subroutine scam_setopts( scmlat_in, scmlon_in,iopfile_in,single_column_in, &
   character(len=*), intent(in), optional :: scm_clubb_iop_name_in
   real(r8), intent(in), optional       :: scm_relaxation_low_in
   real(r8), intent(in), optional       :: scm_relaxation_high_in  
+  logical, intent(in), optional        :: scm_zero_non_iop_tracers_in
   integer ncid,latdimid,londimid,latsiz,lonsiz,latid,lonid,ret,i
   integer latidx,lonidx
   real(r8) ioplat,ioplon
@@ -296,6 +301,10 @@ subroutine scam_setopts( scmlat_in, scmlon_in,iopfile_in,single_column_in, &
      scm_clubb_iop_name=scm_clubb_iop_name_in
   endif
 
+  if (present (scm_zero_non_iop_tracers_in)) then
+     scm_zero_non_iop_tracers=scm_zero_non_iop_tracers_in
+  endif
+
   if (present (iopfile_in)) then
      iopfile=trim(iopfile_in)
   endif

components/eam/src/dynamics/eul/eul_single_column_mod.F90

@@ -20,6 +20,8 @@ module eul_single_column_mod
 
 subroutine scm_setinitial
 
+  use constituents, only: pcnst, qmin
+
   implicit none
 
   integer i, j, k, thelev
@@ -51,6 +53,9 @@ subroutine scm_setinitial
     endif
 
     if (get_nstep() .eq. 0) then
+      do i = 1, pcnst
+         if (scm_zero_non_iop_tracers) q3(1,:,i,1,n3) = qmin(i)
+      end do
       do k=thelev,PLEV
         if (have_t) t3(1,k,1,n3)=tobs(k)
         if (have_q) q3(1,k,1,1,n3)=qobs(k)

components/eam/src/dynamics/se/se_single_column_mod.F90

@@ -5,7 +5,7 @@ module se_single_column_mod
 
 use element_mod, only: element_t
 use scamMod
-use constituents, only: cnst_get_ind
+use constituents, only: cnst_get_ind, pcnst
 use dimensions_mod, only: nelemd, np
 use time_manager, only: get_nstep, dtime, is_first_step
 use ppgrid, only: begchunk
@@ -27,11 +27,13 @@ module se_single_column_mod
 
 subroutine scm_setinitial(elem)
 
+  use constituents, only: qmin
+
   implicit none
 
   type(element_t), intent(inout) :: elem(:)
 
-  integer i, j, k, ie, thelev
+  integer i, j, k, cix, ie, thelev
   integer inumliq, inumice, icldliq, icldice
 
   if (.not. use_replay .and. get_nstep() .eq. 0) then
@@ -74,6 +76,9 @@ subroutine scm_setinitial(elem)
           endif
 
           if (get_nstep() .eq. 0) then
+            do cix = 1, pcnst
+               if (scm_zero_non_iop_tracers) elem(ie)%state%Q(i,j,:,cix) = qmin(cix)
+            end do
             do k=thelev, PLEV
 #ifdef MODEL_THETA_L
               if (have_t) elem(ie)%derived%FT(i,j,k)=tobs(k)
@@ -132,7 +137,6 @@ subroutine apply_SC_forcing(elem,hvcoord,tl,n,t_before_advance,nets,nete)
     use element_mod, only : element_t
     use physical_constants, only : Cp, Rgas, cpwater_vapor
     use time_mod
-    use constituents, only: pcnst
     use time_manager, only: get_nstep
     use shr_const_mod, only: SHR_CONST_PI