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Refactor and enhance CMIP7 namelist process (#287)
Summary: Refactor and enhance CMIP7 namelist process Contributors: gold2718 Reviewers: @Ovewh, @mvertens Purpose of changes: Turn CMIP7 data request into usermods - #286 Github PR URL: #287 Changes made to build system: None Changes made to the namelist: None except for new usermods options Changes to the defaults for the boundary datasets: None Substantial timing or memory changes: None Detailed description of changes - Implement configuration file for usermods sets - Add support for output with COSP and/or Aerocom fields - Add support for separate CAM field request (added to CMIP7 request) - Rewrote README.md file - Add regression test for full output (modify base NHIST test) - Improve extract_master_list.py to allow multiple input logs plus user-defined output file. - Create fixed list for CAM fields that do not have addfld calls. These fields are available but are not added to any fincl as their output is hard coded. - Create set of fields for emission-driven runs - Use chemistry diags for a specific package, not from master list - Parse history handling flags from spreadsheets (e.g., CMIP7 data request) - Update PUMAS tag with NCAL bug fix - Update CMIP7 spreadsheet to 2026-07-02:09:05 - Improve reporting of missing fields (introduce verbose option) - Add script to test output - Add docosp = .true. for COSP usermods runs - Implement configuration file for usermods sets - Add support for output with COSP and/or Aerocom fields - Add support for separate CAM field request (added to CMIP7 request) Testing: - aux_cam_noresm on Olivia: All pass except for namelist and output changes for modified test - aux_cam_noresm on Betzy: All pass except for namelist and output changes for modified test
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‎.gitmodules‎

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[submodule "pumas"]
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path = src/physics/pumas
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url = https://github.com/NorESMhub/PUMAS
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fxtag = noresm3_0_005_pumas_v1_38
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fxtag = noresm3_0_006_pumas_v1_38
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fxrequired = AlwaysRequired
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fxDONOTUSEurl = https://github.com/NorESMhub/PUMAS
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‎cime_config/testdefs/testlist_cam.xml‎

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<!-- CAM-Nor test-supported COMPSETS -->
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<!-- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ -->
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<test compset="NFHIST" grid="ne16pg3_ne16pg3_mtn14" name="ERP_D_Ld3" testmods="cam/outfrq1d">
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<test compset="NFHIST" grid="ne16pg3_ne16pg3_mtn14" name="ERP_D_Ld3" testmods="cam/outfrq1d_fulloutput">
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<machines>
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<machine name="betzy" compiler="intel" category="aux_cam_noresm"/>
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<machine name="olivia" compiler="intel" category="aux_cam_noresm"/>

‎cime_config/testdefs/testmods_dirs/cam/outfrq1d_fulloutput/include_user_mods‎

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../../../../usermods_dirs/CMIP7_HistoryHF

‎cime_config/testdefs/testmods_dirs/cam/outfrq1d_fulloutput/user_nl_cam‎

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write_nstep0 = .true.
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inithist = 'ENDOFRUN'

‎cime_config/testdefs/testmods_dirs/cam/outfrq1d_fulloutput/user_nl_clm‎

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!----------------------------------------------------------------------------------
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! Users should add all user specific namelist changes below in the form of
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! namelist_var = new_namelist_value
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!
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! Include namelist variables for drv_flds_in ONLY if -megan and/or -drydep options
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! are set in the CLM_NAMELIST_OPTS env variable.
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!
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! EXCEPTIONS:
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! Set use_cndv by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting
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! Set use_vichydro by the compset you use and the CLM_BLDNML_OPTS -vichydro setting
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! Set use_cn by the compset you use and CLM_BLDNML_OPTS -bgc setting
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! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting
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! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting
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! Set irrigate by the CLM_BLDNML_OPTS -irrig setting
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! Set dtime with L_NCPL option
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! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options
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! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases
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! (includes $inst_string for multi-ensemble cases)
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! Set glc_grid with CISM_GRID option
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! Set glc_smb with GLC_SMB option
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! Set maxpatch_glcmec with GLC_NEC option
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! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable
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!----------------------------------------------------------------------------------
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hist_nhtfrq = -24
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hist_mfilt = 1
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hist_ndens = 1
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‎cime_config/usermods_dirs/CMIP7_COSP/include_user_mods‎

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‎cime_config/usermods_dirs/CMIP7_COSP/user_nl_cam‎

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‎cime_config/usermods_dirs/CMIP7_History/user_nl_cam‎

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‎cime_config/usermods_dirs/CMIP7_HistoryAerocom/user_nl_cam‎

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! CAM aerocom diagnostic namelist entries
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! Aerocom fields will be output for this run
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use_aerocom = .true.
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! Only output fields listed in this file
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empty_htapes = .true.
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! monthly output
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nhtfrq(1) = 0
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mfilt(1) = 1
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fincl1 = 'A550_BC:A', 'A550_DU:A', 'A550_POM:A', 'A550_SO4:A', 'A550_SS:A',
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'ABS550AL:A', 'AIRMASSL:A', 'AODVVOLC:A', 'AQSO4_H2O2:A', 'AQSO4_O3:A',
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'CCN5:A', 'CCN7:A', 'CCN_B:A', 'CLDHGH:A', 'CLDICE:A', 'CLDLIQ:A', 'CLDLOW:A',
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'CLDMED:A', 'CLDTOT:A', 'CONCLD:A', 'D550_DU:A', 'D550_POM:A', 'D550_SS:A',
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'DAYFOC:A', 'DF_SO2:A', 'DOD550:A', 'EC550AER:A', 'FCTL_B:A', 'FDL:A',
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'FDLC:A', 'FDS:A', 'FLDS:A', 'FLDSC:A', 'FLNS:A', 'FLNT:A', 'FSDSC:A',
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'FSNS:A', 'FSNSC:A', 'FSNT:A', 'FSUTOA:A', 'FUL:A', 'FULC:A', 'GS_H2SO4:A',
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'HO2_aft:A', 'IntHeatTr:A', 'KinEnerTr:A', 'LWCF:A', 'LatHeatTr:A',
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'OD550DRY:A', 'OH_aft:A', 'PBLH:A', 'PRECC:A', 'PRECSC:A', 'PRECSL:A',
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'PRECT:A', 'PS:A', 'PotEnerTr:A', 'Q:A', 'QREFHT:A', 'QRL:A', 'RELHUM:A',
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'RHW:A', 'SO2:A', 'SO4_A1:A', 'SO4_A2:A', 'SO4_AC:A', 'SO4_NA:A', 'SO4_PR:A',
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'SST:A', 'SWCF:A', 'T:A', 'TAUX:A', 'TGCLDIWP:A', 'TREFMNAV:A', 'TROP_P:A',
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'TROP_T:A', 'TROP_Z:A', 'TS:A', 'TotEnerTr:A', 'U10:A', 'U:A', 'WD_A_SO2:A',
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'Z3:A', 'dry_DUST:A', 'dry_SALT:A', 'dry_SULFATE:A', 'emis_BC:A', 'emis_OM:A',
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'emis_SALT:A', 'emis_SO2:A', 'emis_SULFATE:A', 'emis_isoprene:A',
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'emis_monoterp:A', 'isoprene:A', 'mmr_BC:A', 'mmr_OM:A', 'mmr_SALT:A',
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'ozone:A', 'wet_BC:A', 'wet_DUST:A', 'wet_SALT:A', 'wet_SULFATE:A'
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! daily output
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nhtfrq(2) = -24
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mfilt(2) = 30
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fincl2 = 'BC_A:A', 'BC_AC:A', 'BC_AI:A', 'BC_AX:A', 'BC_N:A', 'BC_NI:A',
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'CLOUD:A', 'FLDS:A', 'FLNS:A', 'FSDSC:A', 'FSNSC:A', 'FSUTOA:A', 'FULC:A',
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'LHFLX:A', 'MMR_AH2O:A', 'PRECC:A', 'PRECSC:A', 'PRECSL:A', 'PRECT:A', 'PS:A',
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'PSL:A', 'Q:A', 'QREFHT:A', 'RELHUM:A', 'RHREFHT:A', 'RHW:A', 'SHFLX:A',
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'SO2:A', 'SO4_A1:A', 'SO4_A2:A', 'SO4_AC:A', 'SO4_NA:A', 'SO4_PR:A',
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'SOA_A1:A', 'SOA_NA:A', 'SST:A', 'T700:A', 'T850:A', 'TAUX:A', 'TREFMNAV:A',
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'TS:A', 'U010:A', 'U850:A', 'U:A', 'V850:A', 'cb_ozone_c:A', 'mmr_BC:A',
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'mmr_DUST:A', 'mmr_OM:A', 'mmr_SALT:A', 'mmr_SULFATE:A'

‎cime_config/usermods_dirs/CMIP7_HistoryAerocomESM/user_nl_cam‎

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! CAM aerocom_esm diagnostic namelist entries
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! Aerocom fields will be output for this run
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use_aerocom = .true.
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! Only output fields listed in this file
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empty_htapes = .true.
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! monthly output
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nhtfrq(1) = 0
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mfilt(1) = 1
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fincl1 = 'A550_BC:A', 'A550_DU:A', 'A550_POM:A', 'A550_SO4:A', 'A550_SS:A',
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'ABS550AL:A', 'AIRMASSL:A', 'AODVVOLC:A', 'AQSO4_H2O2:A', 'AQSO4_O3:A',
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'CCN5:A', 'CCN7:A', 'CCN_B:A', 'CLDHGH:A', 'CLDICE:A', 'CLDLIQ:A', 'CLDLOW:A',
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'CLDMED:A', 'CLDTOT:A', 'CO2:A', 'CONCLD:A', 'D550_DU:A', 'D550_POM:A',
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'D550_SS:A', 'DAYFOC:A', 'DF_SO2:A', 'DOD550:A', 'EC550AER:A', 'FCTL_B:A',
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'FDL:A', 'FDLC:A', 'FDS:A', 'FLDS:A', 'FLDSC:A', 'FLNS:A', 'FLNT:A',
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'FSDSC:A', 'FSNS:A', 'FSNSC:A', 'FSNT:A', 'FSUTOA:A', 'FUL:A', 'FULC:A',
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'GS_H2SO4:A', 'HO2_aft:A', 'IntHeatTr:A', 'KinEnerTr:A', 'LWCF:A',
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'LatHeatTr:A', 'OD550DRY:A', 'OH_aft:A', 'PBLH:A', 'PRECC:A', 'PRECSC:A',
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'PRECSL:A', 'PRECT:A', 'PS:A', 'PotEnerTr:A', 'Q:A', 'QREFHT:A', 'QRL:A',
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'RELHUM:A', 'RHW:A', 'SO2:A', 'SO4_A1:A', 'SO4_A2:A', 'SO4_AC:A', 'SO4_NA:A',
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'SO4_PR:A', 'SST:A', 'SWCF:A', 'T:A', 'TAUX:A', 'TGCLDIWP:A', 'TREFMNAV:A',
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'TROP_P:A', 'TROP_T:A', 'TROP_Z:A', 'TS:A', 'TotEnerTr:A', 'U10:A', 'U:A',
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'WD_A_SO2:A', 'Z3:A', 'dry_DUST:A', 'dry_SALT:A', 'dry_SULFATE:A',
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'emis_BC:A', 'emis_OM:A', 'emis_SALT:A', 'emis_SO2:A', 'emis_SULFATE:A',
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'emis_isoprene:A', 'emis_monoterp:A', 'isoprene:A', 'mmr_BC:A', 'mmr_OM:A',
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'mmr_SALT:A', 'ozone:A', 'wet_BC:A', 'wet_DUST:A', 'wet_SALT:A',
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'wet_SULFATE:A'
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! daily output
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nhtfrq(2) = -24
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mfilt(2) = 30
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fincl2 = 'BC_A:A', 'BC_AC:A', 'BC_AI:A', 'BC_AX:A', 'BC_N:A', 'BC_NI:A',
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'CLOUD:A', 'FLDS:A', 'FLNS:A', 'FSDSC:A', 'FSNSC:A', 'FSUTOA:A', 'FULC:A',
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'LHFLX:A', 'MMR_AH2O:A', 'PRECC:A', 'PRECSC:A', 'PRECSL:A', 'PRECT:A', 'PS:A',
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'PSL:A', 'Q:A', 'QREFHT:A', 'RELHUM:A', 'RHREFHT:A', 'RHW:A', 'SHFLX:A',
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'SO2:A', 'SO4_A1:A', 'SO4_A2:A', 'SO4_AC:A', 'SO4_NA:A', 'SO4_PR:A',
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'SOA_A1:A', 'SOA_NA:A', 'SST:A', 'T700:A', 'T850:A', 'TAUX:A', 'TREFMNAV:A',
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'TS:A', 'U010:A', 'U850:A', 'U:A', 'V850:A', 'cb_ozone_c:A', 'mmr_BC:A',
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'mmr_DUST:A', 'mmr_OM:A', 'mmr_SALT:A', 'mmr_SULFATE:A'

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