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gckpp_Monitor\u000a (1) solsym needs to be defined explicitely, as it is parsed at compile\u000a time.\u000aFeat: Update .exclude to now include input_mod and pops_mod.F90\u000aFeat: Changes required to make GEOS-Chem 13.0 work with CESM\u000aFeat: Set State_Met%Salinity and Iodide to 0. Will be read from HEMCO\u000aFeat: Compute isLand/Water/Ice/Snow after AirQnt + Get fields from HEMCO\u000a (1) Get IODIDE surface concentration and SALINITY from HEMCO\u000aFeat: Kludge gaseous species names to match CESM restart file:\u000a (1) Bromine, chlorine, iodine and lumped species are not in CESM restart\u000a file. We can choose to load these from a GEOS-Chem restart file but\u000a this is future work.\u000aFeat: Rename CAM's drydep_mod to aer_drydep_mod\u000aFeat: Print dep. lists when getting from namelist\u000aFeat: Allow MAM to compile with CESM-GC\u000aFeat: Remove unused use statement\u000aFeat: Updates to make MAM4 interchange data with CESM-GC\u000a Compile time changes:\u000a (1) prescribe_aerosols is set to FALSE when $chem contains geoschem\u000a (2) Replace aerosol deposition species with MAM4 aerosols in nml files\u000a (3) Remove pp_geoschem/aero_model. Currently, GEOS-Chem only works\u000a with MAM(4) turned on. If MAM is to be switched off in the future,\u000a then the compiler should choose to compile pp_geoschem/aero_model\u000a (which is just a dummy, almost empty file) over\u000a modal_aero/aero_model.F90\u000a Code changes:\u000a (1) Make xname_massptr a public and protected variable. It is used to\u000a establish a mapping between MAM4 and GEOS-Chem aerosols\u000a (2) Add map2MAM4(:,:) in chem_mods and set number of fixed species to\u000a 6 rather than 4\u000a (3) Add dummy constituents for GEOS-Chem aerosols. Ideally, aerosols\u000a that are inherited from MAM should not need to be defined as a\u000a constituent. For instance, BCPI is inherited from bc_a* whereas\u000a NIT is not included and needs to be defined as a constituent (in\u000a order to be advected)\u000a (4) Establish mapping between MAM4 and GEOS-Chem aerosols. Currently,\u000a POM and SOA are not mapped. More work is needed here to figure out\u000a which GEOS-Chem aerosols should be used to map those.\u000a (5) Reverse mapping (aka from GEOS-Chem back to MAM) is not established\u000a yet.\u000a (6) Clip QI and QL to 1.0E-05 as low values (I have found values as low\u000a as 1.0E-141) can make GEOS-Chem blow up in sulfate_mod.\u000a (7) Add empty m_spc_id.F90, required by MAM4\u000a (8) In mo_chem_utils, replace tracerNames by tracname. This is required\u000a as MAM aerosols are not in tracerNames (which only includes\u000a GEOS-Chem species). Add get_inv_ndx. I believe that this change\u000a temporarily breaks dry deposition as performed by MOZART. More\u000a investigation is needed here.\u000a (9) Add subroutine in mo_drydep to load in land types which is required\u000a for MAM4 to perform its own dry deposition\u000a (10) Add MAM4 aerosols to solsym and define inv_lst (list of fixed\u000a species)\u000a ----\u000a TODOs:\u000a (1) Establish reverse mappings (GEOS-Chem -> MAM4)\u000a (2) Check MOZART's dry deposition routines.\u000a (3) As of right now, MAM4 performs dry deposition. Would it be possible\u000a to let GEOS-Chem perform dry deposition of aerosols?\u000a (4) What to do regarding pure GEOS-Chem aerosols (e.g. NIT)?\u000aChore: Fix indentation + capitalization\u000aFeat: Add option to get land types from HEMCO\u000aFix: Aerosol mapping requires more indices in MMR_Beg.\u000aRemove custom emissions\u000aFeat: Add emissions to CESM-GC\u000aFix: Prevent emissions from adding up in CESM-GC. Reset cam_in%cflx\u000aFeat: Modify aero_model.F90 to let GEOS-Chem handle its own aerosols\u000aFix: Resolve circular dependency\u000aFeat: Rename HCO_surf_salinity to HCO_salinity\u000a (1) The physics buffer does not allow to store strings as long as\u000a `HCO_surf_salinity` and would, for instance, store\u000a `HCO_surf_salinit`. To avoid confusion, we rename it to\u000a `HCO_salinity`, same for `HCO_iodide`.\u000aFeat: Allow CESM-GC to output dry deposition velocity used by GEOS-Chem\u000a (1) Add addfld and outfld statements for each dry deposition species,\u000a using State_Chm%DryDepVel\u000a (2) Fix to let chemistry.F90 when LANDTYPE_HEMCO is 1.\u000aFeat: Uncomment call to DO_MIXING to allow for dry deposition\u000aFeat: Change IC condition file\u000a (1) Renamed some species into their GEOS-Chem equivalent. This new IC\u000a file is a mere copy of the default file, with some species renamed\u000aFix: Replace species number with `gas_pcnst`\u000aFeat: Reindexed GEOS-Chem species: tracers, MAM aerosols, SL species\u000a (1) This reindexing is necessary as MAM requires that there is a linear\u000a mapping (constant offset) between solsym and constituents.\u000a (2) adv_mass is now properly defined in mo_sim_dat, using GEOS-Chem\u000a values for all species, except MAM aerosols.\u000aFeat: Add runtime option to using GEOS-Chem wet deposition\u000aFeat: Add files to allow for NEU wet deposition scheme\u000a (1) Add mo_neu_wetdep (copied from MOZART)\u000a (2) Add additional files (mo_mean_mass, mo_setinv, gas_wetdep_opts)\u000a (3) Add new field in mo_neu_wetdep (WDRATE), corresponding to the wet\u000a removal rate in kg/s\u000aFeat: Add NEU WD routines + MAM gas-aerosol exchange\u000a ( 1) Added NEU wet deposition routines. Option to choose between NEU and\u000a GEOS-Chem wet deposition scheme is available at runtime. See commit\u000a #a8d642c\u000a ( 2) Added diagnostic fields for wet deposition. These match the names\u000a of the same quantities in MOZART\u000a ( 3) Added MAM gas-aerosol exchange\u000a ( 4) Rename field DDVel and SurfFlux into DepVel and DepFlux. Might need\u000a to change those in the future to match those in MOZART\u000a ( 5) Established MAM4 aerosol to GEOS-Chem species mapping based on\u000a discussion with Louisa Emmons\u000a ( 6) Added inverse mapping map2GCinv hat maps tracers onto constituent.\u000a This is now used in chem_emissions.\u000a ( 7) Added map2chm which maps solsym onto GEOS-Chem species and\u000a constituents\u000a ( 8) Remove special handlings when defining constituents. Variable names\u000a are now changed in the IC file.\u000a ( 9) Compute CSZAmid field\u000a (10) Fix bug where qH2O was flipped vertically\u000aFeat: Get UVALBEDO from HEMCO\u000a *CAM only defines albedo during daytime. However, UVALBEDO is only used\u000a for photolysis, which should be fine.\u000aFeat: Define MaxTrop/StratLev from grid + Add Set_H2O_Trac\u000aFeat: Add OH and JRates diagnostics.\u000aFeat: Get H2O mmr from specific humidity\u000a (1) GEOS-Chem's water mass mixing ratio is derived from CAM's specific\u000a humidity\u000a (2) Additionally, the JRates diagnostics are only computed if they are\u000a an output field\u000aChore: Remove unnecessary comment\u000aFix: Unit check failed because 'kg/ kg dry' /= 'kg/kg dry'\u000aFeat: Remove special handlings as we now use GEOS-Chem IC\u000a (1) Previously GEOS-Chem species were modified to account for the\u000a species in the CAM restart file (e.g. HNO2 vs HONO). Now, we just\u000a use GEOS-Chem initial conditions that have been regridded to\u000a ~0.9x1.25\u000aFeat: Add option to pass H2O tendency to Q + change some addfld\u000aFeat: Set State_Met%OMEGA equal to state%omega\u000aFeat: Allow CESM-GC to compute overhead ozone from State_Chm%Species\u000aFeat: Allow CESM-GC runs to be restartable\u000aFeat: Implement 3-D emissions.\u000a (1) Surface emissions (layer PVER) are passed to cam_in%cflx while the\u000a non-surface emissions are added directly to the chemical tendencies\u000a (2) Dry deposition fluxes are now passed to cam_in%cflx such that:\u000a cam_in%cflx = eflx - dflx\u000a (3) Remove call to DO_MIXING as this is now handled by CAM.\u000aFeat: Replace tracerNames with solsym in chem_implements_cnst\u000aFeat: Changes required by GEOS-Chem 13.0.0\u000aFeat: Move compile time flags to run time flags for DD velocities\u000aFeat: Read OMOC from HEMCO and store in State_Chm\u000aFeat: Move all GEOS-Chem related diagnostics to cesmgc_diag_mod.F90\u000aFeat: Add missing initialization of ThisLoc and ErrMsg\u000aFeat: Add option to output State_Met in cesmgc_diag_mod.F90\u000aFeat: Update GEOS-Chem branch in Externals_CAM.cfg to be `CESM`\u000aFeat: Replace pp_geoschem with geoschem\u000aFeat: Reset MAM-inherited aerosols to 0 before mapping\u000a (1) Resetting MAM-inherited aerosols in State_Chm%Species allows these\u000a aerosols to not accumulate over time. Otherwise, we would have\u000a for instance:\u000a BCPI = BCPI + MAM4,\u000a which would accumulate overtime if BCPI was not reset\u000a (2) Lowered the threshold on QI and QL to 1.0E-10 rather than 1.0E-05\u000aFeat: Add MAM aerosols to cesmgc_diag_mod\u000aFeat: Add lightning emissions\u000aFeat: Add MEGAN emissions\u000aFeat: Symbolic link to mozart/mo_lightning\u000aFeat: Add symbolic link to MOZART files, rather than copy\u000aFeat: Add lightning, MEGAN, aerosol and fire emissions\u000aFeat: Remote WDRATE_* from CAM history fields\u000aFix: Molar weight pFe\u000aFix: Add to_upper to tracerNames, required since 'pFe' /= 'PFE'\u000aChore: Try lower and uppercase tracernames when getting data from pbuf\u000aFix: Handle cases where ncol /= pcols\u000aChore: Add note explaining why DQRLSAN needs to be zero in top layer\u000aFeat: Pass GEOS-Chem aerosol emissions to MAM tendencies\u000aFix: Fix typo SO4S vs SOAS\u000aFeat: Enforce lq('Q') to be true if passing H2O tendencies:\u000a (1) lq(cQ) = .True. if applyQTend is True\u000a (2) iFirstCnst is now a variable in chem_mods\u000a (3) Reset cam_in%cflx for all species (including MAM aerosols)\u000aFeat: Only diagnose wet deposition rates of soluble species\u000aFeat: Skip emissions on first time step before HEMCO fills in data\u000aFeat: Add chem_is-like function in mo_chm_utls\u000aFix: Fix typo\u000aFeat: Add or rename some output fields:\u000a (1) Add option to save out chemical tendencies (kg/kg/s or kg/s)\u000a (2) Rename output fluxes to match CAM-Chem\u000aFeat: Add _CLFX and other CAM-Chem like diagnostics to CESM-GC\u000aFeat: Add new GC compsets that mimic CAM-Chem compsets:\u000a (1) New compsets\u000a (2) Enforce NTHRDS_ATM to be 1 when running with GEOS-Chem\u000aFeat: Add new use_cases XML entries for newly added GC compsets\u000aFeat: Turn on rad_prog_ozone for GEOS-Chem chemistry\u000aFeat: Implement CAM-Chem like diagnostics for CESM-GC:\u000a (1) Rename diagnostics to match CAM-Chem's\u000a (2) Only perform diagnostics computations if field is an output.\u000a Use hist_fld_active whenever a call to outfld is performed.\u000aFeat: Make sure that GC's SOAGX species is not picked up by MAM\u000aFix: Remove debug statement in cesmgc_diag_mod\u000aFeat: Add mmr tendencies for MAM aerosols from chemistry\u000aFeat: Replace DO loops with array element-wise operations\u000aFeat: Set NTHRDS_*=1 when using a GEOS-Chem compset\u000aFeat: Make SDYN compset with GEOS-Chem have 56 levs\u000aFeat: Pass chemical tendencies to MAM aerosols:\u000a (1) Changes in aerosol concentrations due to GEOS-Chem processing is\u000a now passed to chemical tendencies for MAM aerosols\u000a (2) Wet deposition of MAM-inherited aerosols is not performed in\u000a GEOS-Chem. To do so, we define a new logical `WD_ExternalDep` in\u000a SpcInfo\u000aFeat: Remove mass-weighted OH concentration diagnostics\u000aFeat: Add CO2 as constituent\u000aFeat: Compute CO2 chemical tendencies:\u000a (1) GEOS-Chem overwrites CO2 concentrations at every time step. We thus\u000a set State_Chm%Species(:,:,:,iCO2) = 0.0e+00 before chemistry and\u000a compute chemical tendencies based on how much CO2 has been produced.\u000a (2) Cleanup\u000aFeat: Apply CAM-Chem surface boundary conditions for long-lived species\u000aFeat: Remove hardwired path to GEOS-Chem CHEM_INPUTS directory\u000aFeat: Remove hard-wired paths for GEOS-Chem inputs:\u000a (1) All input files are now (one-time) copied from geoschem_src/run/CESM\u000a to Buildconf/camconf. Then to the run folder every time builnml is\u000a called\u000aFeat: Read from input.geos\u000aFeat: Read input.geos rather than hard-wiring input options\u000aFeat: Add check to make sure that solsym is following list of GC tracer\u000aChore: Clean up in short_lived_species\u000aFix: Fix wrong reference MMR\u000aChore: Cleanup, remove unused MWRatio and longNames\u000aFeat: Update .exclude to exclude gosat and tccon from GEOS-Chem folder\u000aFeat: Get strat_chem data from HEMCO\u000aFeat: Add timers around DO_CHEMISTRY + Fix diagnostic in WetDep\u000aFeat: Remove PSO4 diagnostic (write statement)\u000aFix: Fix diagnostics of emissions\u000aFeat: Remove option to let GEOS-Chem perform wet scavenging.\u000a (1) The only option to perform convective scavenging in CESM-GC is\u000a currently to rely on the NEU scheme, which handles large-scale\u000a precipitation and convective scavening. Since the variables\u000a required by the GEOS-Chem convective routines cannot be extracted\u000a easily, we rely on the NEU scheme to perform washout due to both\u000a LS precipitation and convective scavenging for gases AND aerosols.\u000a (2) A next commit will follow to specify Henry coefficients of aerosols.\u000a The best option is to probably set something similar as HNO3\u000aFeat: Make non-MAM GC aerosols \"gas-like\" species for wet&dry dep\u000a (1) Move all GC aerosols from aer_drydep_list to drydep_list and from\u000a aer_wetdep_list to gas_wetdep_list (see previous commits too)\u000a (2) This allows to remove the 'GC_AER_' terminology for GC aerosols\u000a (3) Aerosol emission fluxes (e.g. BCPI) are now passed directly to\u000a MAM (e.g. flux to bc_a4). This allows for the removal of some\u000a interfacing code in cesmgc_emissions_mod.F90\u000a (4) Fix diagnostic naming issues (e.g. replaced WD_HBR with WD_HBr)\u000a (5) Remove extra bit of code in cesmgc_diag_mod dealing with wet dep\u000a in GEOS-Chem, which had been removed in previous commits\u000a (6) In mo_neu_wetdep.F90, make all GC aerosols be removed like HNO3\u000a (7) Revert previous changes in modal_aero that used to deal with\u000a GC aerosols in aer_drydep_list\u000a\u000aSigned-off-by: Thibaud Fritz \u000a", "date" : "2021-12-07 13:10:05 -0700", "id" : "9a9ead503679507c872b20ce2aa5665c8ea6c974", "msg" : "Squashed 60+ commits from Thibaud Fritz", "paths" : [ { "editType" : "edit", "file" : "bld/namelist_files/use_cases/geoschem.xml" }, { "editType" : "add", "file" : "src/chemistry/geoschem/m_spc_id.F90" }, { "editType" : "add", "file" : "src/chemistry/aerosol/aer_drydep_mod.F90" }, { "editType" : "add", "file" : "bld/namelist_files/use_cases/hist_geoschem.xml" }, { 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