fix some issues in derecho regression tests

	modified:   bld/build-namelist
	modified:   bld/namelist_files/namelist_defaults_cam.xml
	modified:   bld/namelist_files/namelist_definition.xml
	modified:   bld/namelist_files/use_cases/2010_cam6.xml
	modified:   bld/namelist_files/use_cases/sd_cam6.xml
	modified:   bld/namelist_files/use_cases/waccm_sc_1850_cam6.xml
	modified:   src/chemistry/geoschem/chemistry.F90
	modified:   src/chemistry/pp_terminator/chemistry.F90
	modified:   src/control/camsrfexch.F90

bld/build-namelist

@@ -509,6 +509,19 @@ if ($phys_mode_flags > 1) {
 my $simple_phys = 0;
 if ($adia_mode or $ideal_mode) { $simple_phys = 1; }
 
+# Setup default ndep streams only if not simple_phys or aqua_mode and
+# the chemistry cannot produce the nitrogen depostion fluxes
+if (!($simple_phys or $aqua_mode)) {
+  my $chem_nitrodep = chem_has_species($cfg, 'NO') and chem_has_species($cfg, 'NH3');
+  if (!$chem_nitrodep) {
+    add_default($nl, 'stream_ndep_data_filename');
+    add_default($nl, 'stream_ndep_mesh_filename');
+    add_default($nl, 'stream_ndep_year_first');
+    add_default($nl, 'stream_ndep_year_last');
+    add_default($nl, 'stream_ndep_year_align');
+  }
+}
+
 # Single column mode
 my $scam = $cfg->get('scam');
 my $scam_iop = $cfg->get('scam_iop');

bld/namelist_files/namelist_defaults_cam.xml

@@ -2063,6 +2063,9 @@
 <!-- nitrogen deposition to surface models -->
 <stream_ndep_data_filename>lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc</stream_ndep_data_filename>
 <stream_ndep_mesh_filename>share/meshes/fv0.9x1.25_141008_polemod_ESMFmesh.nc</stream_ndep_mesh_filename>
+<stream_ndep_year_first sim_year="1850-2000">1850</stream_ndep_year_first>
+<stream_ndep_year_last sim_year="1850-2000">2015</stream_ndep_year_last>
+<stream_ndep_year_align sim_year="1850-2000">1850</stream_ndep_year_align>
 <stream_ndep_year_first>2000</stream_ndep_year_first>
 <stream_ndep_year_last>2000</stream_ndep_year_last>
 <stream_ndep_year_align>1</stream_ndep_year_align>

bld/namelist_files/namelist_definition.xml

@@ -7609,6 +7609,12 @@ Bubble-mediated sea-air transfer. See ocean_emis.F90 for details.
 Default: FALSE
 </entry>
 
+<entry id="ndep_list" type="char*16(2)" category="Nitrogen Deposition"
+       group="ndep_inparm" valid_values="" >
+List of nitrogen deposition fluxes to be sent from CAM to surface models.
+Default: set by build-namelist.
+</entry>
+
 <entry id="stream_ndep_year_first" type="integer" category="Nitrogen Deposition"
        group="ndep_stream_nl" valid_values="" >
 Year first to use in nitrogen deposition stream data.

bld/namelist_files/use_cases/2010_cam6.xml

@@ -83,4 +83,8 @@
 <flbc_type>      'CYCLICAL'                          </flbc_type>
 <flbc_cycle_yr>  2010                                </flbc_cycle_yr>
 
+<stream_ndep_year_first>2010</stream_ndep_year_first>
+<stream_ndep_year_last>2010</stream_ndep_year_last>
+<stream_ndep_year_align>1</stream_ndep_year_align>
+
 </namelist_defaults>

bld/namelist_files/use_cases/sd_cam6.xml

@@ -28,12 +28,16 @@
 
   <prescribed_strataero_type    >     'SERIAL'                                                                     </prescribed_strataero_type>
   <prescribed_strataero_datapath>     'atm/cam/ozone_strataero'                                                    </prescribed_strataero_datapath>
-  <prescribed_strataero_file>         'ozone_strataero_WACCM_L70_zm5day_18500101-20150103_CMIP6ensAvg_c180923.nc'  </prescribed_strataero_file> 
+  <prescribed_strataero_file>         'ozone_strataero_WACCM_L70_zm5day_18500101-20150103_CMIP6ensAvg_c180923.nc'  </prescribed_strataero_file>
   <prescribed_strataero_use_chemtrop> .true.                                                                       </prescribed_strataero_use_chemtrop>
 
   <scenario_ghg            >    'CHEM_LBC_FILE'   </scenario_ghg>
   <flbc_file>atm/waccm/lb/LBC_1750-2015_CMIP6_GlobAnnAvg_c180926.nc</flbc_file>
   <flbc_type>'SERIAL'</flbc_type>
   <flbc_list>'CO2','CH4','N2O','CFC11eq','CFC12'</flbc_list>
 
+  <stream_ndep_year_first>1850</stream_ndep_year_first>
+  <stream_ndep_year_last>2015</stream_ndep_year_last>
+  <stream_ndep_year_align>1850</stream_ndep_year_align>
+
 </namelist_defaults>

bld/namelist_files/use_cases/waccm_sc_1850_cam6.xml

@@ -88,4 +88,11 @@
  'UTEND4', 'UTEND5', 'FRONTGF', 'FRONTGFA', 'EKGW', 'QNO', 'QRLNLTE', 'QRL_TOT', 'DUV', 'DVV', 'TTPXMLC'
 </fexcl1>
 
+<!-- prescribed nitrogen deposition fluxes -->
+<stream_ndep_data_filename>lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc</stream_ndep_data_filename>
+<stream_ndep_mesh_filename>share/meshes/fv0.9x1.25_141008_polemod_ESMFmesh.nc</stream_ndep_mesh_filename>
+<stream_ndep_year_first>1850</stream_ndep_year_first>
+<stream_ndep_year_last>1850</stream_ndep_year_last>
+<stream_ndep_year_align>1</stream_ndep_year_align>
+
 </namelist_defaults>

src/chemistry/geoschem/chemistry.F90

@@ -22,7 +22,7 @@ module chemistry
 #if defined( MODAL_AERO )
   use modal_aero_data,     only : ntot_amode
 #endif
-  
+
   ! GEOS-Chem derived types
   USE DiagList_Mod,         ONLY : DgnList          ! Diagnostics list object
   use GeosChem_History_Mod, ONLY : HistoryConfigObj ! History diagnostic object
@@ -59,6 +59,7 @@ module chemistry
   public :: chem_readnl                    ! read chem namelist
   public :: chem_emissions
   public :: chem_timestep_init
+  public :: chem_has_ndep_flx
 
   !
   ! Private routines:
@@ -166,6 +167,8 @@ module chemistry
   ! For dry deposition
   character(len=shr_kind_cl) :: depvel_lnd_file = 'depvel_lnd_file'
 
+  ! for nitrogen deposition fluxes to surface models
+  logical, parameter :: chem_has_ndep_flx = .false.
 
 contains
 
@@ -515,11 +518,11 @@ subroutine chem_register
     CALL cnst_get_ind('Q',     cQ,     abort=.True.)
     CALL cnst_get_ind('H2O',   cH2O,   abort=.True.)
     CALL cnst_get_ind('H2SO4', cH2SO4, abort=.True.)
- 
+
     !------------------------------------------------------------
     ! Get mapping between dry deposition species and species set
     !------------------------------------------------------------
-    
+
     nIgnored = 0
 
     if (debug .and. masterproc) write(iulog,'(a,i4,a)') 'chem_register: looping over gas dry deposition list with ', nddvels, ' species'
@@ -831,7 +834,7 @@ subroutine chem_readnl(nlfile)
        ! Now go through the KPP mechanism and add any species not
        ! implemented by the tracer list in geoschem_config.yml
        !----------------------------------------------------------
-       
+
        IF ( nSpec > nSlsMax ) THEN
           CALL ENDRUN('chem_readnl: too many species - increase nSlsmax')
        ENDIF
@@ -1022,7 +1025,7 @@ subroutine chem_init(phys_state, pbuf2d)
     use Time_Mod,              only : Accept_External_Date_Time
     use Ucx_Mod,               only : Init_Ucx
     use Unitconv_Mod,          only : MOLES_SPECIES_PER_MOLES_DRY_AIR
-    use Vdiff_Mod,             only : Max_PblHt_For_Vdiff 
+    use Vdiff_Mod,             only : Max_PblHt_For_Vdiff
 
     TYPE(physics_state),                INTENT(IN   ) :: phys_state(BEGCHUNK:ENDCHUNK)
     TYPE(physics_buffer_desc), POINTER, INTENT(INOUT) :: pbuf2d(:,:)
@@ -1143,7 +1146,7 @@ subroutine chem_init(phys_state, pbuf2d)
     ! on State_Grid(BEGCHUNK).
     ! To go around this, we define all of GEOS-Chem arrays with
     ! size PCOLS x PVER, which is the largest possible number of
-    ! grid cells. 
+    ! grid cells.
     CALL Init_State_Grid( Input_Opt  = Input_Opt, &
                           State_Grid = maxGrid,   &
                           RC         = RC        )
@@ -1484,7 +1487,7 @@ subroutine chem_init(phys_state, pbuf2d)
        ! Init_Drydep
        ! Thibaud M. Fritz - 04 Mar 2020
        !----------------------------------------------------------
-       
+
        ALLOCATE(map2GC_dryDep(nddvels), STAT=IERR)
        IF ( IERR .NE. 0 ) CALL ENDRUN('Failed to allocate map2GC_dryDep')
 
@@ -1754,7 +1757,7 @@ subroutine chem_timestep_init(phys_state, pbuf2d)
     use mo_flbc,           only : flbc_chk
     use mo_ghg_chem,       only : ghg_chem_timestep_init
     use physics_buffer,    only : physics_buffer_desc
-    
+
     TYPE(physics_state), INTENT(IN):: phys_state(begchunk:endchunk)
     TYPE(physics_buffer_desc), POINTER :: pbuf2d(:,:)
 
@@ -2019,7 +2022,7 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
     REAL(r8)          :: mmr_tend(state%NCOL,PVER,gas_pcnst)
     REAL(r8)          :: wk_out(state%NCOL)
     LOGICAL           :: Found
-    
+
     CHARACTER(LEN=shr_kind_cl) :: tagName
 
     REAL(r8), PARAMETER   :: zlnd  = 0.01_r8   ! Roughness length for soil [m]
@@ -2364,7 +2367,7 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
     ENDDO
 
     ! Deal with secondary organic aerosols (SOAs). This mapping is using the
-    ! complex SOA option in GEOS-Chem. 
+    ! complex SOA option in GEOS-Chem.
     ! MAM uses five volatility bins spanning saturation concentrations from 0.01
     ! to 100 ug/m3 (logarithmically). The complex SOA option has four volatility
     ! bins that 0.1 to 100 ug/m3. We lump the lowest two bins in CESM2 to the
@@ -3692,7 +3695,7 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
     ! Compute the surface flux for the non-local mixing,
     ! (which means getting emissions & drydep from HEMCO)
     ! and store it in State_Chm%Surface_Flux
-    ! 
+    !
     ! For CESM-GC, Surface_Flux will be equal to the opposite of the
     ! dry deposition flux since emissions are loaded externally
     ! ( SurfaceFlux = eflx - dflx = - dflx )
@@ -3739,10 +3742,10 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
           ! Get the species ID from the drydep ID
           N = State_Chm(BEGCHUNK)%Map_DryDep(ND)
           IF ( N <= 0 ) CYCLE
-   
+
           M = map2GCinv(N)
           IF ( M <= 0 ) CYCLE
-   
+
           cam_in%cflx(1:nY,M) = cam_in%cflx(1:nY,M) &
                               + State_Chm(LCHNK)%SurfaceFlux(1,1:nY,N)
        ENDDO
@@ -3763,7 +3766,7 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
                             new_units      = KG_SPECIES_PER_M2,  &
                             previous_units = previous_units,     &
                             RC             = RC                    )
- 
+
 
     IF ( RC /= GC_SUCCESS ) THEN
        ErrMsg = 'Error encountered in "Convert_Spc_Units"!'

src/chemistry/pp_terminator/chemistry.F90

@@ -32,9 +32,10 @@ module chemistry
   public :: chem_write_restart
   public :: chem_read_restart
   public :: chem_init_restart
-  public :: chem_readnl                    ! read chem namelist 
+  public :: chem_readnl                    ! read chem namelist
   public :: chem_reset_fluxes
   public :: chem_emissions
+  public :: chem_has_ndep_flx
 
   interface chem_write_restart
      module procedure chem_write_restart_bin
@@ -45,9 +46,11 @@ module chemistry
      module procedure chem_read_restart_pio
   end interface
 
+  logical, parameter :: chem_has_ndep_flx = .false.
+
   ! Private data
   integer, parameter :: nspecies = 3
-  
+
   integer :: idx_cl =-1
   integer :: idx_cl2=-1
 
@@ -75,21 +78,21 @@ end function chem_is
 !================================================================================================
 
   subroutine chem_register
-    !----------------------------------------------------------------------- 
-    ! 
+    !-----------------------------------------------------------------------
+    !
     ! Purpose: register advected constituents for parameterized greenhouse gas chemistry
-    ! 
+    !
     !-----------------------------------------------------------------------
 
     real(r8), parameter :: cptmp = 666._r8
     real(r8), parameter :: qmin = -1.e36_r8
 
     logical :: camout
     integer :: i, n
-    
+
     do i = 1, nspecies
        camout = trim(species(i)) .eq. 'RHO'
-       call cnst_add( species(i), adv_mass(i), cptmp, qmin, n, &  
+       call cnst_add( species(i), adv_mass(i), cptmp, qmin, n, &
                       readiv=.true.,mixtype='dry',cam_outfld=camout)
        indices(i) = n
        map2chm(n) = i
@@ -123,12 +126,12 @@ end function chem_is_active
 !================================================================================================
 
   function chem_implements_cnst(name)
-    !----------------------------------------------------------------------- 
-    ! 
+    !-----------------------------------------------------------------------
+    !
     ! Purpose: return true if specified constituent is implemented by this package
-    ! 
+    !
     ! Author: B. Eaton
-    ! 
+    !
     !-----------------------------------------------------------------------
     implicit none
     !-----------------------------Arguments---------------------------------
@@ -137,7 +140,7 @@ function chem_implements_cnst(name)
     logical :: chem_implements_cnst        ! return value
 
     integer :: i
-    
+
     chem_implements_cnst = .false.
 
     do i = 1, nspecies
@@ -150,13 +153,13 @@ function chem_implements_cnst(name)
   end function chem_implements_cnst
 
 !===============================================================================
-  
+
   subroutine chem_init(phys_state, pbuf2d)
-    !----------------------------------------------------------------------- 
-    ! 
+    !-----------------------------------------------------------------------
+    !
     ! Purpose: initialize parameterized greenhouse gas chemistry
     !          (declare history variables)
-    ! 
+    !
     !-----------------------------------------------------------------------
     use physics_buffer, only: physics_buffer_desc
     use cam_history,    only: addfld, add_default, horiz_only
@@ -196,7 +199,7 @@ end subroutine chem_init
   subroutine chem_timestep_init(phys_state, pbuf2d)
     use physics_buffer,   only: physics_buffer_desc
 
-    type(physics_state), intent(in):: phys_state(begchunk:endchunk)                 
+    type(physics_state), intent(in):: phys_state(begchunk:endchunk)
     type(physics_buffer_desc), pointer :: pbuf2d(:,:)
 
   end subroutine chem_timestep_init
@@ -222,7 +225,7 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dt, pbuf,  fh2o )
     real(r8), optional,  intent(out)   :: fh2o(pcols) ! h2o flux to balance source from chemistry
 
     real(r8) :: a(pver),b(pver),c(pver),d(pver)
-    
+
     real(r8) :: k1(pcols)
     real(r8) :: k2(pcols)
 
@@ -278,7 +281,7 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dt, pbuf,  fh2o )
            l(i,:) = (1._r8 - e(i,:))/det(i,:)/dt
         elsewhere
            l(i,:) = 4._r8*k2(i)
-        endwhere 
+        endwhere
 
         cl_f(i,:) = -l(i,:)*(cl(i,:) - det(i,:) + r(i) )*(cl(i,:) + det(i,:) + r(i)) / ( 1._r8 +e(i,:) + dt*l(i,:)*(cl(i,:) + r(i)))
         cl2_f(i,:) = -cl_f(i,:) / 2._r8
@@ -325,7 +328,7 @@ subroutine chem_init_cnst(name, latvals, lonvals, mask, q)
     real(r8)            :: q_vmr(size(q, 1)) !  volume mixing ratio (ncol)
     real(r8)            :: det(size(q, 1))
     real(r8)            :: krat(size(q, 1))
-    
+
     real(r8)            :: k1(size(q, 1))
     real(r8)            :: k2(size(q, 1))
 
@@ -347,7 +350,7 @@ subroutine chem_init_cnst(name, latvals, lonvals, mask, q)
     krat(:) = k1(:) / (4._r8 * k2(:))
 
     h = init_vmr_cl + 2._r8 * init_vmr_cl2
-    
+
     det(:) = sqrt(krat(:) * krat(:) + 2._r8 * h * krat(:))
 
     if (trim(name) == trim(species(1)) ) then
@@ -412,15 +415,15 @@ subroutine chem_init_restart(File)
   end subroutine chem_init_restart
 !================================================================================
   subroutine chem_reset_fluxes( fptr, cam_in )
-    use camsrfexch, only : cam_in_t     
+    use camsrfexch, only : cam_in_t
 
     real(r8), pointer             :: fptr(:,:)        ! pointer into    array data
     type(cam_in_t), intent(inout) :: cam_in(begchunk:endchunk)
 
   end subroutine chem_reset_fluxes
 !================================================================================
   subroutine chem_emissions( state, cam_in, pbuf )
-    use camsrfexch,       only: cam_in_t     
+    use camsrfexch,       only: cam_in_t
     use physics_buffer,   only: physics_buffer_desc
 
     ! Arguments:

src/control/camsrfexch.F90

@@ -9,7 +9,7 @@ module camsrfexch
   use constituents,    only: pcnst
   use ppgrid,          only: pcols, begchunk, endchunk
   use phys_grid,       only: get_ncols_p, phys_grid_initialized
-  use infnan,          only: nan, posinf, assignment(=)
+  use infnan,          only: posinf, assignment(=)
   use cam_abortutils,  only: endrun
   use cam_logfile,     only: iulog
   use srf_field_check, only: active_Sl_ram1, active_Sl_fv, active_Sl_soilw,                &
@@ -329,11 +329,11 @@ subroutine atm2hub_alloc( cam_out )
 
           allocate (cam_out(c)%nhx_nitrogen_flx(pcols), stat=ierror)
           if ( ierror /= 0 ) call endrun(sub//': allocation error nhx_nitrogen_flx')
-          cam_out(c)%nhx_nitrogen_flx(:) = nan
+          cam_out(c)%nhx_nitrogen_flx(:) = 0._r8
 
           allocate (cam_out(c)%noy_nitrogen_flx(pcols), stat=ierror)
           if ( ierror /= 0 ) call endrun(sub//': allocation error noy_nitrogen_flx')
-          cam_out(c)%noy_nitrogen_flx(:) = nan
+          cam_out(c)%noy_nitrogen_flx(:) = 0._r8
 
        endif