Changes

Feat: Changes to include GEOS-Chem as a chemistry option for CESM

(1) This introduces an option to compile GEOS-Chem src files.

(2) Interface is inexistant so far

(3) CAM still uses the Terminator chem package to satisfy dependencies

Reproducing commit from MSL - Jan 19, 2018

Squashed of 50+ commits from Thibaud Fritz

Feat: Update config files to include GEOS-Chem option for CAM
 (1) Update config files in cam/bld/
 (2) Update config files in cam/cime_config
Feat: Add customized chemistry.F90 for GEOS-Chem:
  *Reproducing commit from MSL - Mar 6, 2018
Feat: Initial implementation of compilable code
 (1) The code can now be compiled using a CAM 4.0 + "dummy" GEOS-Chem
     component set (compset FGC). This is based on the "tropospheric
     mozart" set.
  *Reproducing commit from SDE - May 17, 2018
Feat: Make radiatively-active species into chemical constituants
 (1) Added N2O, CH4, CFC11, CFC12
Feat: Get tracers and species from input.geos and KPP
 (1) Tracer lists are now acquired from the input files and from the
     pre-built KPP mechanism
  *Reproducing commit from SDE - May 19, 2018
Feat: Add additional flags when compiling GEOS-Chem
Fix: Update folder name following version 12.6.0
Feat: Allocate major state variables (Input, Met, Chem)
 (1) Allocating GEOS-Chem state variables
 (2) Setting input.geos path as a module variable
  *Reproducing commit from SDE - May 19, 2018
Chore: Cleanup and capitalization
Feat: Initialize core GEOS-Chem modules
 (1) Initializes ChmState, GrdState and MetState objects
 (2) Grid objects are currently initialized identically. However, they
     should be chunk-dependent. The grids are set based on the lat/lon
     edges for now, using GEOS-Chem's SetGridFromCtrEdges subroutine
 (3) Initializes Input_Opt
 (4) Added subroutine to update time-steps within GEOS-Chem
 (5) Added error trapping statements
Feat: Add initialization of Linoz module and passing CHEM_INPUTS
 (1) Initializing Linoz module
 (2) Passing CHEM_INPUTS to Input_Opt
 (3) Remove incorrect overwrite of NTracers
Feat: Initialize and cleanup State_Chm and State_Met
Feat: Initialize Drydep_Mod
 (1) Initialize Drydep_Mod
 (2) Update .exclude file to include GeosCore/drydep_mod.F
Feat: Add Init_Error to chem_init for GEOS-Chem
Feat: Initialize and cleanup GEOS-Chem modules
 (1) Add calls to module initialization and cleanup subroutines
 (2) Update .exclude file
Feat: Get grid area and Ap and Bp values from CAM
 (1) Get grid area from CAM interface
 (2) Pass CAM's Ap and Bp values to GEOS-Chem's Pressure_Mod
 (3) Call to Cleanup_Pressure
Feat: Affect data to State_Chm
Feat: Initialize chemistry, add missing cleanup routines
Feat: Initialize pressure transfer
Feat: Add first call to chemistry
Feat: Register all tracers using species database
 (1) Register species
 (2) Initial step towards the update of State_Met
Feat: Fill key variables in State_Met
Feat: Add PBL height transfer capability
 (1) Enforce lat/lonMidArr to be R4 not FP
Feat: Enforce correct tracer registration
Feat: Add initialization of short-lived species
Feat: Update surface area during chemistry loop
Feat: Use reference MMRs when queried for ICs
 (1) Zero reference MMRs at initialization
 (2) Use reference MMRs when queried for initial conditions
Feat: Groundwork for correctly reporing H2O tendencies
 (1) Add indices to key species
Feat: Add all advected species to output
 (1) Add advected species to output
 (2) Force precision of H2O to be r8
 (3) Fixed capitalization of variables
Feat: Make short-lived species persist between time steps
Feat: Set GEOS-Chem data from CAM
 (1) Date information is now propagated to GEOS-Chem. Algorithm needs
     tweaking (seems to give a date 1 minute earlier than it should).
     Also currently force the year to be 2000 as the default CAM year
     is 0000.
Feat: Disable stratospheric aerosols in GEOS-Chem
Feat: Progate more met fields to State_Met using CAM data
Feat: Change NY to PCOLS for consistency and add step count tracking
Feat: Increased default list of diagnostics for GEOS-Chem
Feat: Implement GEOS-Chem wet deposition + Estimate of 2D cloudiness
 (1) Implemented GEOS-Chem wet deposition
 (2) CAM does not provide an estimate of 2D cloud cover, so we use an
     estimate (maximum 3D cloudiness in vertical column). This matches
     the technique originally used for GCAP in GEOS-Chem.
 (3) Fix Z0 not being assigned
Feat: Move SLS information to chem_mods + Emission module
 (1) Move tracer and SLS information out to chem_mods
 (2) Added temporary NO source to provide useful output
 (3) Initial code stub for an emissions module
Fix: Fix reading of tracers in input.geos
 (1) Tracers in input.geos
 (2) Fix indentation
Chore: Now compiling GEOS-Chem with -DMODEL_
Feat: Added wet/(dry) deposition. See more comments below!
 (01) Added definition of MaxTropLev, MaxStratLev and MaxChemLev. This
      will require some additional thought
 (02) As of right now, Linoz is turned off as the current grid doesn't
      extend past 30 km, causing segmentation when running with Linoz
      turned on
 (03) Added code that's commented out right now for future development
       (HEMCO, Olson landmap, convection, ...)
 (04) Added field descrition and unit of State_Met variables when
      converted from CESM to State_Met
 (05) Updated compution of cloud optical depth. Following what MOZART
      does.
 (06) Now correctly initializing InChemGrid to .True. everywhere
 (07) Added newDay, newMonth variables
 (08) Added wet deposition
 (09) Added dry deposition. However, it is purely a software right now,
      as it runs without initializing land types
 (10) Uniformization of variables
Chore: Remove debug
Feat: Deal with compile-time definition of GEOS-Chem dry dep. species
 (1) Update ChemNamelist to be able to read deposition species from .xml
     files and filtering these with the species list from mo_sim_dat.F90.
     This last file lists all GEOS-Chem species and is only read at
     compile time and is not compiled since GEOS-Chem tracers and species
     are defined at run time from input.geos and KPP files.
 (2) Update geoschem.xml to now list dry and wet deposition species
Feat: Implement dry deposition in CESM/GC
 (1) Different options are available to compute dry deposition
     velocities:
    1. All deposition velocities are computed from GEOS-Chem using data
       from HEMCO
    2. CLM passes dry deposition velocities over land and ocean and ice
       velocities are computed from GEOS-Chem using data from HEMCO
    3. CLM passes dry deposition velocities over land and ocean and ice
       velocities are computed in a similar way as MOZART
Feat: Add missing file from last commit to replicate MOZART's dry dep. calculations
Feat: Add Externals to download GEOS-Chem source code
Feat: Add mo_chem_utils.F90 required for mo_drydep_mod
Feat: Update .exclude
Feat: Import CLM4.0/4.5/5.0 data and use it for GEOS-Chem
 (1) Import data from CLM
 (2) Add compset to run GEOS-Chem with CLM4.5/5.0
 (3) Add routine getLandTypes to convert CLM to OlsonLandMaps. More work
     is needed to convert CLM4.5 land types
 (4) CAM's building procedure has been modified to include the right
     version of CLM
 (5) Modify .exclude
Style: Fix typos that got introduced when converting commits to fork
Feat: Modify Externals_CAM.cfg to download GEOS-Chem code
Revert "Feat: Modify Externals_CAM.cfg to download GEOS-Chem code"
Feat: Update .gitignore to ignore GEOS-Chem repo

Squashed 5 commits from Haipeng Lin

Feat: Implement HEMCO_CESM within CESM-GC (Initial attempt in syncing CAM sources)
Feat: HEMCO_CESM code integration (full). Add mo_sim_dat and mo_tracname
Fix: Call set_sim_dat from chemistry.F90 to pass solsym to HEMCO_CESM.
Fix: Do not assign other variables within mo_sim_dat -- to discuss
Fix: Comment out mo_sim_dat except solsym, expand solsym size to nTracersMax
*This might not be needed after all as HEMCO_CESM now reads tracer names from chem_mods. But fixing this so it doesn't infinite loop.

Squashed 2 commits from Thibaud Fritz

Feat: Add Olson / CLM land type mapping for CLM4.5/5.0
Feat: Add FAST_JX_DIR in Input_Opt. Remove hard-wired paths in fast_jx

Squashed 4 commits from Lizzie Lundgren

Change GEOS-Chem source to CESM-GC GitHub organization and branch name
Use GEOS-Chem branch feature/13.0.0+CESM
Update HEMCO interfaces directory name in configure
Partial updates to enable GEOS-Chem dev/13.0.0 to build in CESM

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Squashed 60+ commits from Thibaud Fritz

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

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Write ZPJ values for RXN_NO2, RXN_O3_1/2a into HCO_IN_JNO2, HCO_IN_JOH for HEMCO ParaNOx extension.

Fix: fldname_ns fix to FIELDNAME

Squashed 4 commits from Thibaud Fritz

Feat: Uniformize calls to HEMCO
Fix: Replace SO4S with SO4s
Fix: Fix XML file name
Feat: Capitalize all GC constituents name, and other updates:
(1) This is required because boundary conditions are stored with
    capitalized name. I would rather follow the same terminology
    as MOZART (with capitalized constituents) rather than modify
    the interface with flbc.
(2) Update geoschem.xml to match FC2000climo compset
(3) Fix bug where lght_no_prod_factor was not applied in CESM-GC
(4) Set ext_frc_specifier to '' for CESM-GC compsets as we rely on
    HEMCO

Feat: Now retrieve fields from HEMCO using 2-D pbuf fields

Squashed 10 commits from Thibaud Fritz

Fix: Pass surface J-Rates to HEMCO for PARANOX
Fix: Update MMR_Beg for MAM aerosols:
(1) This fix avoids a slow, but steady build up of some MAM aerosols
Fix: Make sure GEOS-Chem (aerosol phase) MSA is not picked up by MAM
Feat: Diagnose constituents as mol/mol apart from MAM aerosols
Feat: Update namelist_defaults s.t. geoschem mimics trop_strat_mam4vbs
Feat: Update geoschem.xml to mimic history_* XML variables
Feat: Add history_* options to save out fields in cesmgc_diag_mod
Feat: Don't make solsym fixed size, but rather of size gas_pcnst
Feat: Change nadv_chem from 240 to 238
Feat: Add more history_* options to save out fields (mimic CAM-Chem)

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Feat: Retrieve ParaNOx deposition fluxes from HEMCO

Squashed 18 commits from Thibaud Fritz

Feat: Revert mo_drydep to MOZART's version + Update chemistry.F90
 (1) Note that most of the mo_drydep routines are unused. We only need
     to load in landtypes for MAM
Feat: Add aerosol number emissions in CESM-GC
 (1) Emission diameters are taken from:
     Emmons, Louisa K., et al. "The chemistry mechanism in the
     Community Earth System Model version 2 (CESM2)."
     Journal of Advances in Modeling Earth Systems 12.4 (2020).
Feat: Lump GEOS-Chem SO4 with so4_a* and H2SO4
Fix: Remove hard-wired number emissions as this has been moved to HEMCO
Feat: Update .xml files with GEOS-Chem chemistry (MEGAN)
Feat: Add MEGAN emissions with GEOS-Chem species
Fix: Update IF condition for SRF diagnostics
Feat: Add hemco_nl in build-namelist
Feat: Rename geoschem.xml to 2000_geoscheml.xml (FC2000climo_GC)
Feat: Add 2010_geoscheml.xml (FC2010climo_GC)
Feat: Update config_component to reflect recent changes to xml files
Feat: Add SOA mapping between MAM and GEOS-Chem complex SOA option
 (1) Add mapping
 (2) Extend number of constituents
Feat: Add AEIC organic species to external forcings list
Feat: Add GEOS-Chem surface boundary conditions
Feat: Update .gitignore to exclude GEOS-Chem source code
Fix: Fix for sulfur mapping between CESM2 and GEOS-Chem
 (1) SO4_gasRatio and binRatio are in mol/mol, not kg/kg
Feat: Update .exclude for GEOS-Chem 13.1
Fix: Update in-cloud opticaldepth with cloud fractions

Fix: correct improper merge conflict handling introduced during rebase

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Feat: Return in sox_cldaero_mod if running with GEOS-Chem

This prevents the code from double counting in-cloud sulfur oxidation

Signed-off-by: Thibaud Fritz <fritzt@mit.edu>

Fix: correct wrong indexes introduced by manual revert; rm GC wetscav

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Added coefficient arrays used to compute the horizontal gradients of
cell-centered variables to the input and restart streams for the
MPAS dynamical core.

Added MPAS mesh information and coefficients for computing
the frontogenesis function to the dynamics export state
for use in d_p_coupling (where the frontogenesis function
and angle are computed).

Added the option to compute the frontogenesis function and the
angle of del(theta) needed by the gravity-wave drag parameterization.

Enable compilation in CESM 2.3 for non-GEOS-Chem case

This commit includes:
 1. Syntax bug fixes in perl file ChemNamelist.pm
 2. Setting perl smartmatch to experimental in ChemNamelist.pm to avoid
    perl version dependent build error for use of '~~' (checks if item
    is in array)
 3. Remove CAM imports lwtgcell, pwtgcell, and lai that are used for
    GEOS-Chem dry deposition velocity calculation. In a future update
    GEOS-Chem will no longer calculate dry deposition velocity when run
    in CESM so these imports are not needed.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Build fixes for CESM-GC within CESM: non-GEOS-Chem cases

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update GEOS-Chem interface code for compatibility with CESM 2.3

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Fix bug in J-value diagnostic names for O3O1D

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Remove remaining references to compset FSPCAMM_GC

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

GEOS-Chem driver routine updates for compatibility with GEOS-Chem 13.3.4

Modifications for new GEOS-Chem species (HMS) in version 13.3

- Added HMS to solsym array and increased length by 1
- Add HMS molecular wt to adv_mass array and increased length by 1
- Increased parameter nTracersMax by 1
- Increased bld/configure variables chem_nadv by 1


Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Use ESCOMP/HEMCO_CESM rather than H. Lin's fork

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Change GEOS-Chem branch name to diverge from version used in CESM-GC 2.1

CESM-GC using CESM 2.1 used GEOS-Chem 13.1. The GEOS-Chem version used in
development for CESM 2.3 is 13.3.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Set default namelist values for cam_physics_mesh in geos-chem use cases

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Bug fix: increase module parameter gas_pcnst by 1 to include HMS

This is necessary after upgrading the GEOS-Chem version since HMS is
a newly added advected gas species.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Modifications to turn off dry deposition and dependencies on CLM for land

Kludge to get by missing Henry's Law coeffs for certain species

Configure compsets that use GEOS-Chem to also use HEMCO

Added high-level log prints

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Use same RUN_STARTDATE for compset FCHIST_GC as used in FCHIST

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Revert hist_geoschem.xml to original; will adjust in user_nl_cam

Remove compset that uses geoschem_mam3

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

No diff updates to GEOS-Chem use cases to document diffs with non-GC

Also deleted unused use case defined in geoschem_baro_moist.xml

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

committing changes toward running caram_dust with SE Dycode

Clean up GEOS-Chem compset namelists

-Move megan_specifier definition for GEOS-Chem in use_cases files to
 bld/build-namelist given chem=geoschem
-Move cam_physics_mesh definitions used by HEMCO from use_cases files to
 namelist_defaults_cam.xml
-Remove drydep_method, ext_frc_*, and srf_emis_* parameters from
 GEOS-Chem use case files
-Delete namelist file (geoschem_baro_moist.xml) for unused GEOS-Chem
 compset
-Set default RUN_STARTDATE for the GEOS-Chem climo compsets in
 config_compsets.xml
-Remove ext_frc_* and srf_emis_* variables from geoschem/chemistry.F90
 since not used
-Fix incorrect comment in mo_chem_utls.F90

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Move GEOS-Chem deposition lists to common file with namelist defaults

This update also slims down the dry deposition lists to not include
aerosols or unused species (new lists submitted by Haipeng Lin).

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Updates to Neu wet dep in GEOS-Chem for Henry's Law coeffs from netcdf

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update Neu wet dep debug prints in GEOS-Chem

Debug prints are now only done by the master processor. The debug logical
is still manually set in mo_neu_wetdep.F90. It is false by default.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Preliminary updates for GEOS-Chem 14.0

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Add debug print option within GEOS-Chem chemistry.F90

Currently set to true by default.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

changes for unstructured grids

	modified:   Externals_CAM.cfg
	modified:   bld/namelist_files/namelist_defaults_cam.xml
	modified:   cime_config/testdefs/testmods_dirs/cam/carma_dust/user_nl_cam
	modified:   cime_config/testdefs/testmods_dirs/cam/carma_meteor_impact/user_nl_cam
	modified:   cime_config/testdefs/testmods_dirs/cam/carma_mixed_sulfate/user_nl_cam
	modified:   cime_config/testdefs/testmods_dirs/cam/carma_pmc/user_nl_cam
	modified:   src/physics/cam/physpkg.F90
	modified:   src/physics/carma/cam/carma_constants_mod.F90
	modified:   src/physics/carma/cam/carma_getH2O.F90
	modified:   src/physics/carma/cam/carma_getH2SO4.F90
	modified:   src/physics/carma/cam/carma_getT.F90
	modified:   src/physics/carma/cam/carma_intr.F90
	modified:   src/physics/carma/models/cirrus/carma_model_mod.F90
	modified:   src/physics/carma/models/dust/carma_model_mod.F90
	modified:   src/physics/carma/models/meteor_impact/carma_model_mod.F90
	modified:   src/physics/carma/models/sea_salt/carma_model_mod.F90

add izumi_nag carma tests

Fixes for using GEOS-Chem 14.0

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Updates to get gas-phase dry deposition when using GEOS-Chem to run

Gas-phase dry deposition using GEOS-Chem is not yet validated.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

read cell_gradient_coefs from IC file only if front GWs are turn on; cold start CLM in mpasa480 test; clean up

        modified:   cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa480/shell_commands
        modified:   src/dynamics/mpas/dp_coupling.F90
        modified:   src/dynamics/mpas/driver/cam_mpas_subdriver.F90

add cheyenne tests

ignore fixedinit issues with SE dycore; revert carma_get profile routines

        modified:   cime_config/testdefs/testmods_dirs/cam/carma_pmc/user_nl_cam
        modified:   src/physics/carma/cam/carma_getH2O.F90
        modified:   src/physics/carma/cam/carma_getH2SO4.F90
        modified:   src/physics/carma/cam/carma_getT.F90

Turn on frontogenesis GWs in WACCM-SC; add cheyenne tests

        modified:   Externals_CAM.cfg
        modified:   bld/namelist_files/namelist_defaults_cam.xml
        modified:   cime_config/config_pes.xml
        modified:   cime_config/testdefs/testlist_cam.xml
        modified:   src/dynamics/mpas/driver/cam_mpas_subdriver.F90
        modified:   src/dynamics/mpas/dyn_comp.F90

fix restarts by haloing tracers; append constants with _r8 kind

        modified:   src/dynamics/mpas/dp_coupling.F90

some code clean up

	modified:   src/dynamics/mpas/dp_coupling.F90
	modified:   src/dynamics/mpas/driver/cam_mpas_subdriver.F90
	modified:   src/dynamics/mpas/dyn_comp.F90
	modified:   src/dynamics/mpas/dyn_grid.F90

Change geoschem .exclude file to use relative paths to files

Previously file only contained filenames. This update should be used with
CIME updates submitted in:
ESMCI/cime#4180
ESMCI/cime#4302

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Clean up new debug print code in physpkg.F90

Local debug option can be enabled in the source code to print messages
before and after chem_timestep_tend and aero_model_drydep are called.
Prints are off by default.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Expand error prints in constituents module for clarify

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Remove online land type option when using GEOS-Chem and use Olson/XLAI

Dry deposition in GEOS-Chem now uses a combination of CLM dry deposition
velocities and GEOS-Chem computed velocities which is determined by
presence of ocean (100% CLM velocities if no ocean, 100% GEOS-Chem
velocities if all ocean, and a scaled value of the two if in between).
This update also uncomments several code that set State_Met fields, and
the logicals for CLM drydep vel and online land type is removed (the
former is effectively now always true and the latter is always false).

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update GEOS-Chem chemistry log messages for clarity

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Remove unused code from GEOS-Chem chemistry.F90 file

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Externals update to use latest GEOS-Chem, HEMCO_CESM, and HEMCO

These will need to change again before merge because GEOS-Chem 14.0.0
and HEMCO 3.5.0 are not yet released, and I am now using my fork of
HEMCO_CESM with modifications needed to link to and build latest HEMCO
as is.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Temporarily put wetdep and drydep lists in namelist file per GEOS-Chem case

This is until there is a better way to handle the wetdep and drydep
lists for GEOS-Chem cases

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Add deposition coefficient data file to GEOS-Chem use case files

Eventually this will go higher up in the cam bld directory since the
same file is used for all GEOS-Chem cases.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Minor edit to Neu wet deposition debug code when using GEOS-Chem

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Add non-advected GEOS-Chem species OH and HO2 to solsym for diagnostics

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Change default FCSD_GC year from 2005 to 2015

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Fix parameters incremented for non-advected species added to solysm

Only gas_pcnst should be incremented when adding non-advected species to
solsym.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Change Default FCHIST_GC run startdate year from 2010 t0 2015

This avoids an error retrieving CEDS emissions for which 2010 is not
available.

This update also include a minor comment change in chem_mods.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Add friction velocity as a nuopc import in CAM

Ustar is used in GEOS-Chem dry deposition over ocean

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

use carma base tag carma4_01; misc cleanup

        modified:   Externals_CAM.cfg
        modified:   src/physics/carma/models/dust/carma_model_mod.F90
        modified:   src/physics/carma/models/meteor_impact/carma_model_mod.F90
        modified:   src/physics/carma/models/meteor_smoke/carma_model_mod.F90
        modified:   src/physics/carma/models/mixed_sulfate/carma_model_mod.F90
        modified:   src/physics/carma/models/pmc/carma_model_mod.F90
        modified:   src/physics/carma/models/sea_salt/carma_model_mod.F90
        modified:   src/physics/carma/models/sulfate/carma_model_mod.F90
        modified:   src/physics/carma/models/test_growth/carma_model_mod.F90
        modified:   src/physics/carma/models/test_passive/carma_model_mod.F90
        modified:   src/physics/carma/models/test_radiative/carma_model_mod.F90
        modified:   src/physics/carma/models/test_swelling/carma_model_mod.F90
        modified:   src/physics/carma/models/test_tracers/carma_model_mod.F90
        modified:   src/physics/carma/models/test_tracers2/carma_model_mod.F90

correct dry dep history field description; misc cleanup

        modified:   src/physics/carma/cam/carma_constants_mod.F90
        modified:   src/physics/carma/cam/carma_intr.F90

set ubc_specifier for waccm_ma_sulfur chemistry

        modified:   cime_config/testdefs/testmods_dirs/cam/carma_mixed_sulfate/user_nl_cam
        modified:   cime_config/testdefs/testmods_dirs/cam/carma_sulfate/user_nl_cam

Add hemco_grid_xdim, hemco_grid_ydim namelist variables to configure HEMCO grid.

Update HEMCO tag to hemco-cesm1_0_hemco3_5_0

Experimental first version of New History Diagnostics

Disable legacy Jval_ approach; new history diags with debug (wip)

Fix diagnostic chunk bug; now functional

Update HEMCO external to 3.5.1

Add FCnudged_GC component set based on FCnudged.

Add hist_geoschem_nudged.xml configuration for FCnudged_GC

Remove config_compsets.xml change that does not belong to this branch and was added in error

Expand CAM history field name maximum to 32 chars

Fix bug that was forcing HEMCO_Config.rc as hemco_config_file

Fix typo in HEMCO-CESM tag

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

fix bug in Z3GM diagnostic

	modified:   src/ionosphere/waccmx/ionosphere_interface.F90

Added coefficient arrays used to compute the horizontal gradients of
cell-centered variables to the input and restart streams for the
MPAS dynamical core.

Added MPAS mesh information and coefficients for computing
the frontogenesis function to the dynamics export state
for use in d_p_coupling (where the frontogenesis function
and angle are computed).

Added the option to compute the frontogenesis function and the
angle of del(theta) needed by the gravity-wave drag parameterization.

read cell_gradient_coefs from IC file only if front GWs are turn on; cold start CLM in mpasa480 test; clean up

        modified:   cime_config/testdefs/testmods_dirs/cam/outfrq9s_mpasa480/shell_commands
        modified:   src/dynamics/mpas/dp_coupling.F90
        modified:   src/dynamics/mpas/driver/cam_mpas_subdriver.F90

Turn on frontogenesis GWs in WACCM-SC; add cheyenne tests

        modified:   Externals_CAM.cfg
        modified:   bld/namelist_files/namelist_defaults_cam.xml
        modified:   cime_config/config_pes.xml
        modified:   cime_config/testdefs/testlist_cam.xml
        modified:   src/dynamics/mpas/driver/cam_mpas_subdriver.F90
        modified:   src/dynamics/mpas/dyn_comp.F90

fix restarts by haloing tracers; append constants with _r8 kind

        modified:   src/dynamics/mpas/dp_coupling.F90

some code clean up

	modified:   src/dynamics/mpas/dp_coupling.F90
	modified:   src/dynamics/mpas/driver/cam_mpas_subdriver.F90
	modified:   src/dynamics/mpas/dyn_comp.F90
	modified:   src/dynamics/mpas/dyn_grid.F90

fix bug in Z3GM diagnostic

	modified:   src/ionosphere/waccmx/ionosphere_interface.F90

Remove debugging routines

Fix HEMCO namelist bugs

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Upgrade GEOS-Chem to version 14.0.1

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>hemco

Fix MEGAN emissions in CESM-GC - active_fall_flxvoc is a logical and not integer

Add comments on xml source

Update comments; remove more debug routines

Remove array temporary allocations; now use one outTmp_3D and outTmp_2D for 3D and 2D data.

Remove unnecessary legacy code in cesmgc_diag_mod.F90

Update comments; remove extraneous GC_FAILURE call to address review comments

Rainbow code changes first pass

Code cleanup, bug fixed

Change CMEPS and coupler remotes from fvitt to ESCOMP github

Francis Vitt's updates required for GEOS-Chem are now merged into the
main development branches and therefore his GitHub branches do not need
to be used.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Initial machine learning code for PUMAS

Update PUMAS external for amk and ank allocations

Reduce GEOS-Chem dir mozart files; build mozart and pp_none if geos-chem

This update required modifications to mozart/mo_chem_utls.F90 to allow
optional argument for comparing upper-case letters in function
get_spc_ndx.

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Initial mods for namelist micro_mg_warm_rain

Removed unused file geoschem/getLandTypes.F90

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Modify mozart module mo_neu_wetdep for use when GEOS-Chem chemistry enabled

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Use mozart chem_prod_loss_diags.F90 rather than copy if GEOS-Chem enabled

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update PUMAS tag

Update PUMAS hash

Modifications to use Mozart short_lived_species module in GEOS-Chem

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Add missing GEOS-Chem diagnostics subroutine calls; cleanup other files

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update GEOS-Chem compset diagnostics list; fix build-namelist permissions

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Update cam_physics_mesh defaults for HEMCO

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>

Various code cleanup

Fix for modal_aer_opt failures

Enclose additional section in check for machine learning code

Draft commit to support HEMCO_CESM v1.1.0.

- Only emissions in extfrc_lst (in mo_sim_dat) will have 3-D emissions now, as only these will have a 3-D pbuf available to save memory. This is accounted for in cesmgc_emissions_mod.F90.
- The list of species with 3-D emissions in GEOS-Chem are now listed in mo_sim_dat.F90.
- The number of species with 3-D emissions (length of extfrc_lst) is now specified in extcnt in chem_mods.F90.

This is a preliminary commit. Further updates are needed to update the HEMCO_CESM external to the appropriate version, as well as moving up to HEMCO 3.6.0.

Update PUMAS external

Add stochastic_collect_tau_cam.F90