ChangeLog start; code clean up; add ndep diags to reg test

	modified:   cime_config/testdefs/testmods_dirs/cam/outfrq9s_Leung_dust/user_nl_cam
	modified:   doc/ChangeLog
	modified:   src/utils/srf_field_check.F90

cime_config/testdefs/testmods_dirs/cam/outfrq9s_Leung_dust/user_nl_cam

@@ -1,6 +1,6 @@
 dust_emis_method = 'Leung_2023'
 
-fincl2 = 'dst_a1SF', 'dst_a2SF', 'dst_a3SF'
+fincl2 = 'dst_a1SF', 'dst_a2SF', 'dst_a3SF',  'a2x_NHXDEP','a2x_NOYDEP'
 
 mfilt=1,1,1,1,1,1
 ndens=1,1,1,1,1,1

doc/ChangeLog

@@ -1,5 +1,136 @@
 ===============================================================
 
+Tag name: cam6_4_???
+Originator(s): fvitt
+Date:
+One-line Summary:
+Github PR URL:
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+
+ Change logical determinations on how to set nitrogen deposition fluxes which are sent to
+ surface models through the NUOPC mediator.  This sets the nitrogen deposition fluxes to
+ prescribed CDEP input stream fluxes if corresponding namelist options are set.  Otherwise,
+ the nitrogen deposition fluxes set to chemistry computed fluxes if the chemistry is capable
+ of providing the fluxes.  (Github issue #1196)
+
+Describe any changes made to build system:
+
+Describe any changes made to the namelist:
+
+List any changes to the defaults for the boundary datasets:
+
+Describe any substantial timing or memory changes:
+
+Code reviewed by:
+
+List all files eliminated:
+
+List all files added and what they do:
+
+List all existing files that have been modified, and describe the changes:
+
+M       bld/build-namelist
+ - change how default ndep_stream namelist options are set
+   . check if chemistry is capable of producing nitrogen deposition fluxes
+   . set defaults only if not simple physics nor aqua-planet configuration
+
+M       bld/namelist_files/namelist_defaults_cam.xml
+ - default ndep_stream namelist settings for perpetual year 2000 configuration
+
+M       bld/namelist_files/namelist_definition.xml
+ - updates to stream_ndep_* namelist descriptions
+
+M       bld/namelist_files/use_cases/1850_cam_lt.xml
+M       bld/namelist_files/use_cases/1850_cam_mt.xml
+M       bld/namelist_files/use_cases/2010_cam6.xml
+M       bld/namelist_files/use_cases/hist_cam_lt.xml
+M       bld/namelist_files/use_cases/hist_cam_mt.xml
+M       bld/namelist_files/use_cases/sd_cam6.xml
+M       bld/namelist_files/use_cases/waccm_sc_1850_cam6.xml
+ - stream_ndep_* namelist settings for use cases
+
+M       cime_config/buildnml
+ - remove the use of CAM_STREAM_NDEP* xml vars to set stream_ndep* namelist options
+
+M       cime_config/config_component.xml
+ - remove CAM_STREAM_NDEP* xml vars
+
+M       src/chemistry/geoschem/chemistry.F90
+M       src/chemistry/pp_none/chemistry.F90
+M       src/chemistry/pp_terminator/chemistry.F90
+ - add chem_has_ndep_flx flag -- set to .FALSE. for these chem pckgs
+
+M       src/chemistry/mozart/chemistry.F90
+ - add chem_has_ndep_flx flag
+ - add check for prescribed nitrogen depostion fluxes
+
+M       src/chemistry/mozart/mo_chm_diags.F90
+ - check for NOy and NHx species in chemistry to determine if
+   chemistry can produce nitrogen deposition fluxes
+
+M       src/control/camsrfexch.F90
+ - allocate cam_out nitro dep flx arrays only if not simple phys and not aqua-planet
+
+M       src/control/runtime_opts.F90
+ - invoke stream_ndep_readnl sooner in the initialization phase -- from read_namelist
+
+M       src/cpl/nuopc/atm_import_export.F90
+ - set out going ndep fluxes only if not simple physics and not aqua-planet
+ - set out going ndep fluxes to prescribed ndep stream fields, otherwise,
+   set chemistry computed fluxes if available.
+
+M       src/cpl/nuopc/atm_stream_ndep.F90
+ - add readnl routine -- seperated from init routine which can be invoked from
+   runtime_opts -- earlier in initialization
+ - set default use_ndep_stream flag to .false.
+
+M       src/physics/cam/cam_diagnostics.F90
+ - add 'a2x_NOYDEP' and 'a2x_NHXDEP' history fields
+
+M       src/utils/srf_field_check.F90
+ - removed active_Faxa_nhx and active_Faxa_noy routine flags which were not useful
+
+If there were any failures reported from running test_driver.sh on any test
+platform, and checkin with these failures has been OK'd by the gatekeeper,
+then copy the lines from the td.*.status files for the failed tests to the
+appropriate machine below.  All failed tests must be justified.
+
+derecho/intel/aux_cam:
+
+derecho/nvhpc/aux_cam:
+
+izumi/nag/aux_cam:
+
+izumi/gnu/aux_cam:
+
+CAM tag used for the baseline comparison tests if different than previous
+tag:
+
+Summarize any changes to answers, i.e.,
+- what code configurations:
+- what platforms/compilers:
+- nature of change (roundoff; larger than roundoff but same climate; new
+  climate):
+
+If bitwise differences were observed, how did you show they were no worse
+than roundoff?
+
+If this tag changes climate describe the run(s) done to evaluate the new
+climate in enough detail that it(they) could be reproduced, i.e.,
+- source tag (all code used must be in the repository):
+- platform/compilers:
+- configure commandline:
+- build-namelist command (or complete namelist):
+- MSS location of output:
+
+MSS location of control simulations used to validate new climate:
+
+URL for AMWG diagnostics output used to validate new climate:
+
+===============================================================
+===============================================================
+
 Tag name: cam6_4_047
 Originator(s): jedwards4b, fvitt
 Date: 19 November 2024

src/utils/srf_field_check.F90

@@ -17,10 +17,6 @@ module srf_field_check
   logical, public, protected :: active_Fall_fco2_lnd = .false.
   logical, public, protected :: active_Faoo_fco2_ocn = .false.
 
-  ! output from atm
-  logical, public, protected :: active_Faxa_nhx = .false.
-  logical, public, protected :: active_Faxa_noy = .false.
-
   public :: set_active_Sl_ram1
   public :: set_active_Sl_fv
   public :: set_active_Sl_soilw