Merge branch 'quantheory:non-iop-tracers-for-pr' into next (PR #5182)

Add scm_zero_non_iop_tracers option

For single-column runs, this sets all tracers in the atmospheric
constituent list to qmin (typically zero) after the initial condition
file (ncdata) is read in, but before the IOP file values are applied.
As a result, non-IOP tracers are initialized to qmin rather than
taking their values from the initial condition file, while IOP-defined
tracers are unaffected.

This option defaults to .false., and hence does not change answers for
existing cases. However, it may be considered safer in the future to
change the default to .true. (at least for non-replay runs), to avoid
inconsistencies between the initial condition file state and the IOP
file state that exacerbate transient spin-up behavior and potentially
bias free-running model results. Like most single column model options,
this option has no effect in global runs.

This PR addresses #5177, at least in part. Actually changing default
behavior for existing SCM cases would require the option to be
enabled in scmlib.

[BFB] no impact on existing tests

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