Short-lived halogen chemistry by fvitt · Pull Request #1470 · ESCOMP/CAM

fvitt · 2026-01-07T15:54:26Z

new file: cime_config/testdefs/testmods_dirs/cam/ts_slh_mam4_outfrq9s/shell_commands new file: cime_config/testdefs/testmods_dirs/cam/ts_slh_mam4_outfrq9s/user_nl_cam new file: cime_config/testdefs/testmods_dirs/cam/ts_slh_mam4_outfrq9s/user_nl_clm new file: cime_config/testdefs/testmods_dirs/cam/wa_slh_mam4_outfrq9s/shell_commands new file: cime_config/testdefs/testmods_dirs/cam/wa_slh_mam4_outfrq9s/user_nl_cam new file: cime_config/testdefs/testmods_dirs/cam/wa_slh_mam4_outfrq9s/user_nl_clm

fvitt · 2026-01-09T19:47:42Z

From @RafaPedroFernandez (CC'd @CAlbertoCuevas):

Please note that I have just made a push for 2 F90 routines in my following GIT:
https://github.com/RafaPedroFernandez/CAM/tree/slh_chemistry_n04_cam6_4_097_rpf

Which is also updated local in derecho:
/glade/u/home/rpfernan/cesm_versions_rpf/derecho_cesm/git_fetch/cesm3_cam6dev_francis/slh_chemistry_n04_cam6_4_097_rpf

Routines are
chemistry.F90:
For SLH, we must call iodine_emissions_srf before the loop to outfld( sflxnam(m), cam_in%cflx(:ncol,m), ncol,lchnk ) in order for SFHOI and SFI2 to be properly written in the output file. If we do not so, the SFHOI and SFI2 are zero in the output file but are somehow included in cam_in%cflx array that is passed to other routines

mo_gas_phase_chmdr.F90
For Iodine washout ... we have always used SAD_ICETROP, which is computed based on CLDICE. This CLDICE was before computed as only ice
cldice(:ncol,k) = q(:ncol,k,cldice_ndx)
and now considers also SNOW
cldice(:ncol,k) = q(:ncol,k,cldice_ndx) + q(:ncol,k,snow_ndx)

Including snow in the variable makes the iodine deposition too efficient, and then we created a new array (ONLYICE) just to compute iodine wet-depositions without affecting other model developments.

modified: src/chemistry/mozart/chemistry.F90 modified: src/chemistry/mozart/mo_gas_phase_chemdr.F90

modified: src/chemistry/mozart/mo_usrrxt.F90

cacraigucar

Partial review - @jimmielin will be reviewing the chemistry section of this PR. My review was on the setup side.

I noticed that there are testing use_cases setup, but I do not see any regression tests being added. Is this an oversight?

cacraigucar · 2026-01-15T23:59:14Z

bld/namelist_files/namelist_defaults_cam.xml

+<xs_short_file>atm/waccm/phot/xs_short_c221005mm_slh_c250930.nc</xs_short_file>
+<xs_long_file >atm/waccm/phot/temp_prs_GT200nm_c221005mm_slh_c250930.nc</xs_long_file>


These two file still need to be "rimport"ed

cacraigucar · 2026-01-16T00:00:52Z

bld/namelist_files/namelist_definition.xml

+<entry id="SSAhno3_ScalingFactor" type="real" category="cam_chem"
+       group="slh_nl" valid_values="" >
+Scaling-factor for SLH Halocarbon surface emissions
+Default: set by build-namelist
+</entry>
+
+<entry id="SSAn2o5_ScalingFactor" type="real" category="cam_chem"
+       group="slh_nl" valid_values="" >
+Scaling-factor for SLH Halocarbon surface emissions
+Default: set by build-namelist
+</entry>
+
+<entry id="LIQfraprx_ScalingFactor_I" type="real" category="cam_chem"
+       group="slh_nl" valid_values="" >
+Scaling-factor for SLH Halocarbon surface emissions
+Default: set by build-namelist
+</entry>
+
+<entry id="ICEfraprx_ScalingFactor_I" type="real" category="cam_chem"
+       group="slh_nl" valid_values="" >
+Scaling-factor for SLH Halocarbon surface emissions
+Default: set by build-namelist
+</entry>
+
+<entry id="ICEfraprx_ScalingFactor_Br" type="real" category="cam_chem"
+       group="slh_nl" valid_values="" >
+Scaling-factor for SLH Halocarbon surface emissions
+Default: set by build-namelist
+</entry>


Comments probably need updating (since they are all the same)

cacraigucar · 2026-01-16T00:05:56Z

cime_config/config_compsets.xml

 	<value  compset="HIST_CAM60%CFIRE">1995-01-01</value>
 	<value  compset="RCP[2468]_CAM\d+">2005-01-01</value>
- 	<value  compset="_CAM.*%NUDG"                   >2010-01-01</value>
+ 	<value  compset="_CAM.*%NUDG"                   >2000-01-01</value>


Why is this PR changing the date for nudging runs?

jimmielin

Thanks @fvitt, I have a few suggested changes but nothing major.

jimmielin · 2026-02-03T16:10:46Z

src/chemistry/mozart/clybryiy_fam.F90

+       wrk(:,:) = cloy( mmr, pcols, ncol )
+
+       factor(:ncol,:) = mmr(:ncol,:,id_cly) / wrk(:ncol,:)


Maybe a safeguard against divide by zero here if wrk(:ncol,:) are close to zero (when cloy initial conditions are very low?)

jimmielin · 2026-02-03T16:11:13Z

src/chemistry/mozart/mo_slh_routines.F90

+!     call mpibcast (SLHemiss_ScalingFactor,      1, mpir8,    0, mpicom)
+!     call mpibcast (ICEfraprx_ScalingFactor,     1, mpir8,    0, mpicom)
+!     call mpibcast (LIQfraprx_ScalingFactor,     1, mpir8,    0, mpicom)


Do these also need to be broadcast?

jimmielin · 2026-02-03T16:12:24Z

src/chemistry/mozart/mo_slh_routines.F90

+!rpf_CESM2_SLH
+!rpf and cac: This threshold is required to aviod huge iodine emissions for low wind peed
+    where ( ws_mask(:ncol) < 3._r8 )
+      ws_mask(:ncol) = 3._r8
+    endwhere
+!rpf_CESM2_SLH


Maybe clean up this comment a bit and fix typos:

Suggested change

!rpf_CESM2_SLH

!rpf and cac: This threshold is required to aviod huge iodine emissions for low wind peed

where ( ws_mask(:ncol) < 3._r8 )

ws_mask(:ncol) = 3._r8

endwhere

!rpf_CESM2_SLH

!rpf and cac: This threshold is required to avoid huge iodine emissions for low wind speeds

where ( ws_mask(:ncol) < 3._r8 )

ws_mask(:ncol) = 3._r8

endwhere

jimmielin · 2026-02-03T16:14:08Z

src/chemistry/mozart/mo_slh_routines.F90

+       !!! Be CAREFULL that if SST = 0 then the division is not possible. Should it be forced to zero?
+       if (ocnfrac(i) == 0) then ! Actually it should be landfrac = 1 ... but we do not want to bring landfrac as an additional agrument
+          iodide_aq(i) = 0 
+       else
+!         iodide_aq(i) = 1.46e6_r8 * exp( -9134._r8 / sst(i) ) * ocnfrac(i)
+          iodide_aq(i) = 1.46e6_r8 * exp( -9134._r8 / sst(i) )
+       end if


Since SST is in Kelvin it shouldn't get close to zero but I would check if it is intended that iodine_aq is computed when sst is below freezing? This may be a science question

jimmielin · 2026-02-03T16:16:24Z

src/chemistry/mozart/mo_slh_routines.F90

+!rpf_CESM2_SLH
+    implicit none
+!rpf_CESM2_SLH


Can be removed since module is declared implicit none

jimmielin · 2026-02-03T16:18:58Z

src/chemistry/mozart/mo_strato_rates.F90

+!rpf_CESM2_SLH
+! I do not include the new rid_# into ids(:) so has_strato_chem condition is not afected
+!rpf_CESM2_SLH


The meaning of "new rid_#" will become unclear after the code is merged in, I would suggest something like

Suggested change

!rpf_CESM2_SLH

! I do not include the new rid_# into ids(:) so has_strato_chem condition is not afected

!rpf_CESM2_SLH

! Short-lived halogen chemistry rid_# (rid_het5_hbr to rid_nat_str_i_4) are not included into ids(:)

! so has_strato_chem condition is not affected.

jimmielin · 2026-02-03T16:20:53Z

src/chemistry/mozart/mo_strato_rates.F90

+                     if ( rid_slf_str_i_2 > 0 ) then
+                        if( hclvmr > small_div .and. hoivmr > small_div ) then
+! CAC 2020 RPF START OF implmentation of the HOI + HCl(liq) =  ICl + H2O  Sulfate Aerosol Reaction
+! NOTE: gprob for HOI species is mapped to gprob_hobr_hcl 
+                           if ( rid_slf_str_i_2 > 0 ) then


The check in line 918 is a duplicate of the check in line 914 for rid_slf_str_i_2 > 0.

jimmielin · 2026-02-03T16:21:02Z

src/chemistry/mozart/mo_strato_rates.F90

+                     if ( rid_slf_str_i_3 > 0 ) then
+                        if( hbrvmr > small_div .and. hoivmr > small_div ) then
+! CAC 2020 RPF START OF implmentation of the HOI + HBr(liq) =  IBr + H2O  Sulfate Aerosol Reaction
+! NOTE: gprob for HOI species is mapped to gprob_hobr_hcl 
+                           if ( rid_slf_str_i_3 > 0 ) then


Same duplicate checks here

jimmielin · 2026-02-03T16:21:11Z

src/chemistry/mozart/mo_strato_rates.F90

+                     if ( rid_slf_str_i_4 > 0 ) then
+                        if( hivmr > small_div .and. hoivmr > small_div ) then
+! CAC 2020 RPF START OF implmentation of the HOI + HI (liq) =  I2  + H2O  Sulfate Aerosol Reaction
+! NOTE: gprob for HOI species is mapped to gprob_hobr_hcl 
+                           if ( rid_slf_str_i_4 > 0 ) then


Same duplicate checks here

jimmielin · 2026-02-03T16:23:51Z

src/chemistry/mozart/mo_usrrxt.F90

+! Is there a typo in the pre-exponential factor? (1.72 instead of 1.73?) Which one is correct?
+!            rxt(:,k,usr_NO2XNO3_M_ndx) = rxt(:,k,tag_NO2_NO3_ndx) * 1.734138e26_r8 * exp_fac(:)
+             rxt(:,k,usr_NO2XNO3_M_ndx) = rxt(:,k,tag_NO2_NO3_ndx) * 1.724138e26_r8 * exp_fac(:)
+!rpf_CESM2_SLH


This comment is leftover and should be checked for correctness

fvitt added 2 commits January 6, 2026 16:06

mods from slh_chemistry branch

628491f

fvitt self-assigned this Jan 7, 2026

cacraigucar requested review from cacraigucar and jimmielin January 7, 2026 17:39

fvitt marked this pull request as draft January 8, 2026 00:09

more changes from Rafa

55f61c9

modified: src/chemistry/mozart/chemistry.F90 modified: src/chemistry/mozart/mo_gas_phase_chemdr.F90

fvitt marked this pull request as ready for review January 13, 2026 23:11

add r8 real kind specifiers

48d7fbd

modified: src/chemistry/mozart/mo_usrrxt.F90

cacraigucar added this to CAM Development Jan 15, 2026

cacraigucar requested changes Jan 16, 2026

View reviewed changes

jimmielin requested changes Feb 3, 2026

View reviewed changes

		<xs_short_file>atm/waccm/phot/xs_short_c221005mm_slh_c250930.nc</xs_short_file>
		<xs_long_file >atm/waccm/phot/temp_prs_GT200nm_c221005mm_slh_c250930.nc</xs_long_file>

		wrk(:,:) = cloy( mmr, pcols, ncol )

		factor(:ncol,:) = mmr(:ncol,:,id_cly) / wrk(:ncol,:)

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fvitt commented Jan 7, 2026

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fvitt commented Jan 9, 2026

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