GMIchem ChangeLog
2020-05-25 <michael.manyin@nasa.gov> Branch: feature/mmanyin/allow_GMI_stubbing
        * Replace routine rcEsmfReadLogical with ESMF_ConfigGetAttribute
        * Eliminate spurious FAIL message from photolysis
        * New boundary condition file

2019-08-15 <michael.manyin@nasa.gov> Tag: Icarus-3_2_p9_MEM_16
        * Added Jules' ship emissions, with some refinements

2019-06-21 <michael.manyin@nasa.gov> Tag: Icarus-3_2_p9_MEM_15
        * CH4 is now a forced boundary condition by default

2019-03-07 <michael.manyin@nasa.gov> Tag: Icarus-3_2_p9_MEM_MERGE_11
        * Split the GMI Run routine into Run1 and Run2.
	* Old Single-Phase mode can still be used, but 2-Phase is the default.

2018-11-29 <michael.manyin@nasa.gov> Tag: Icarus-3_2_p9_MEM_MERGE_8
        * New chemical mechanism with OCS; removed GCO3, GP, GPAN, MVN2

2017-04-05 <jon.e.nielsen@nasa.gov> Tag: Icarus-1_0_JEN_GMI
        * Use runDt to compute chemical tendencies. Divisor gmiDt generates error when
          GMICHEM_DT > RUN_DT and HISTORY collection mode is 'time-averaged'.

2017-01-06 <jon.e.nielsen@nasa.gov> Tag: Heracles-5_3_p3_JEN_GMI-r1
        * Added Mike Manyin's CCMI_REF-C1 and CCMI_REF-C2 updates.
	* Increased N_ = 751 in parm_MIE_fastJX65.h to accomodate at least 132 layers.
        * Replaced km with NVEGTYPE-2 in GmiEmiss_ and GmiDepos_GridCompClassMod.F90 calls to 
          Decode_Land_Types and Decode_XLAI, also for running more than 72 layers.

2016-09-27 <jon.e.nielsen@nasa.gov> Tag: Heracles-5_3_JEN_GMI-v2
	* Includes GOCART::SO4v in optical depth calculation.
	* Added exports for BoxHeight, AIRMASS, NATSAD, ICESAD.
	* Clarified units for QJ, QQJ, QQK, NUMDENS.
	* Added HCl limiter 5 ppbv. Increased condensed HNO3 limit to 25 ppbv.
	* Emission scenarios revised as recommended by Luke Oman.

2016-07-14 <jon.e.nielsen@nasa.gov> Tag: Heracles-5_3_JEN_GMI
	* Correct some fractional photolysis rates in setkin_smv2.h.  From M. Manyin.

2016-06-22 <jon.e.nielsen@nasa.gov> Tag: Heracles-5_2_p1_JEN_GMI
        * Fixed long-standing pressure center/edge issue in FastJX 6.5 implementation
	* Updated strat/trop mechanism to JPL 2010 reaction rates

2016-06-13 <jon.e.nielsen@nasa.gov> Tag: Heracles-5_2_p1_CTM
        * GmiEmiss: Merge M. Manyin's VegLai promotion to Chem_Shared with
          tdt correction in Monitor_T2M.

2016-04-08 <jon.e.nielsen@nasa.gov> Tag: Heracles-5_1_JEN_GMI_p01
        * Rename some emissions imports to resolve ExtData conficts with GOCART
	* Initialize rc in GMI_GridCompMod.F90

2016-03-24 <michael.manyin@nasa.gov> Tag: GEOSagcm_MeM_TR (branch of Heracles-5_1)
        * Remove obsolete emiss_infile_name and emiss_var_name.
        * Replace Using_Daily_Emissions and Daily_Emission_Species with Diurnal_Emission_Species
	* Emissions can now include 3D and 2D (optionally diurnal) fields

2016-02-03 <jon.e.nielsen@nasa.gov> Tag: Heracles-5_1_JEN_GMI
        * Reset default numberNOperFlash to 1.50E+26 in GMI_GridComp.rc.

2016-01-07 <jon.e.nielsen@nasa.gov> Tag: Heracles-4_3_JEN_GMI_p01
        * New GMI_GridComp.rc option: Climatological emissions datasets
          are kg m^{-2} s^{-1} when clim_emiss_by_area: T.

2015-12-09 <jon.e.nielsen@nasa.gov> Tag: Heracles-4_3_JEN_GMI_p01
        * Correct bug in processing and age-off of T2M15d.

2015-09-22 <jon.e.nielsen@nasa.gov> Tag: Heracles-4_3_JEN_GMI
        * Implement Michael Manyin's revision for handling land-type-fractions.

2015-06-11 <jon.e.nielsen@nasa.gov> Tag: Heracles-3_MERRA2-DD_JEN
        * Now using AERO state when GMICHEM is the AERO_PROVIDER.

2015-06-02 <jon.e.nielsen@nasa.gov> Tag: Heracles-3_MERRA2-DD_JEN
        * Now using ExtData.rc instead of Chem_UtilMPread.

2015-04-13 <jon.e.nielsen@nasa.gov> Tag: Heracles-UNSTABLE_JEN_GCC
        * jsparse.F90 replaced with jsparseGMI.F90 to avoid name conflict with GEOSCHEMchem.

2015-04-01 <jon.e.nielsen@nasa.gov> Tag: Heracles-1_0_UNSTABLE_JEN_m2
        * Import DELP from CHEMENV.
        * Update to REPLAY detection.
        * forc_bc_start_num is now the year number for option 2.

2015-02-04 <jon.e.nielsen@nasa.gov> Tag: Ganymed-4_1_JEN_GMI
        * In GmiSAD_GridCompClassMod.F90, opt out of testing HNO3COND when bootstrapping 
          gmichem_import_rst.

2015-01-07 <jon.e.nielsen@nasa.gov> Tag: Ganymed-4_1_JEN_GMI
        * Detect REPLAY to avoid "double counting" when accumulating 15-day time-average T2M.
	* Enable time-dependent GHG and ODS (forc_bc_opt: 2) to accomodate year boundaries
          without modifying forc_bc_start_num in GMI_GridComp.rc.  See GmiUpdateForcingBC_mod.F90
          for details.

2014-06-16 <jon.e.nielsen@nasa.gov> Tag: Ganymed-4_0_BETA11_JEN_GMI
        * Implement more efficient memory use when computing species tendencies.

2014-06-12 <jon.e.nielsen@nasa.gov> Tag: Ganymed-4_0_BETA11_JEN_GMI
        * Replaced ESMF_Bundles with ALLOCATED array for computing species tendencies.

2014-04-25 <jon.e.nielsen@nasa.gov> Tag: Ganymed-4_0_BETA11_JEN
        * Updates for threadsafe from J. Kouatchou.

2013-12-04 <jon.e.nielsen@nasa.gov> Tag: Ganymed-4_0_BETA5_GMI
        * Now using setkin_lchem.h in place of setkin_chem_mech.txt in gmi_acg.pl
          following advice of S. Steenrod that the txt file may become obsolete.
        * Default setting of pr_qqjk is now F (off) to save memory.

2013-09-10 <jon.e.nielsen@nasa.gov> Tag: Ganymed-4_0_UNSTABLE_JEN
        * Implement RUNALARM and GMICHEM_DT.
	* Add amplification/suppression factor for J(NO), default 1.00, recommended by
          Michael Prather and Luke Oman. Reduce to 0.60 if upper stratospheric NOx has a 
          high bias.
        * Reduce lightning NO amplification factor to 0.80 in GMI_GridComp.rc for 5TG/yr, 
          recommended by Luke Oman.

2013-08-14 <jon.e.nielsen@nasa.gov> Tag: Ganymed-4_0_UNSTABLE_JEN
        * Generalize FUNCTION speciesReg_for_CCM for handling more than 123 species in 
          the GMIchem internal state.

2013-07-23 <jon.e.nielsen@nasa.gov> Tag: Ganymed-3_0_p1_GMI
        * Add monthly high-resolution (1/4-degree) CH4 emissions from L. Ott.

2013-06-20 <jon.e.nielsen@nasa.gov> Tag: Ganymed-3_0_p1_GMI
        * Updates for handling FieldBundles under ESMF-5
        * gmi_acg.pl generates transported species names listing

2013-05-24 <jon.e.nielsen@nasa.gov> Tag: Ganymed-2_1_p3_GMI-m2
        * Enable use of EDGAR emission file names with general or specific qualifiers;
          %y4 or 2008, for example.

2013-05-08 <jon.e.nielsen@nasa.gov> Tag: Ganymed-2_1_p3_GMI-m2
        * Add monthly NO and CO fossil-fuel emissions to daily emissions updates.

2013-05-03 <jon.e.nielsen@nasa.gov> Tag: Ganymed-2_1_p3_GMI-m2
        * Enable application of diurnal cycle to daily biomass burning emissions.
        * Allow strat_trop_aerosol as a permitted mechanism identifier (chem_mecha).

2013-04-05 <jon.e.nielsen@nasa.gov> Tag: Ganymed-2_1_p3_GMI-m1
        * Update method used to query units of EM_* export states.
	* Add capability to read daily emission inventory files.
	* Generalize upper pressure limit for application of PSC routines, and
          terminate execution if HNO3COND exceeds a given concentration.
	* Add const_opt = 0, which allows for disabling the fixed concentration species.
	
2013-01-24 <jon.e.nielsen@nasa.gov> Tag: Ganymed-2_0_JEN-m1
        * kgNOx3D from GmiEmissionLightningMod.F90 changed from kg N m^{-3} s^{-1}
          to kg NO m^{-3} s^{-1}. Purpose is to allow comarison to GMI NO_lgt through
          export EM_LGTNO. 

2012-12-11 <jon.e.nielsen@nasa.gov> Tag: Ganymed-2_0_UNSTABLE_JEN-m1
        * Added profiling timers. 

2012-11-28 <jon.e.nielsen@nasa.gov> Tag: Ganymed-2_0_UNSTABLE
        * Eliminated compiler warning "Global name too long" for three strings: 
          GridCompClassMod, GmiPhotolysisRateConstants, and num_qj_o3_to_2oh.
        * OX_TEND in mol mol^{-1} s^{-1}.

2012-09-11 <jon.e.nielsen@nasa.gov> Tag: Ganymed-1_0_JEN-preRelease
        * Allow user to specify a (usually tropical) latitude zone in which condense.F90 
          is not run. The range is -NoPSCZone < lat < NoPSCZone, in degrees.

2012-08-21 <jon.e.nielsen@nasa.gov> Tag: Ganymed-1_0_UNSTABLE_JEN-m4
        * gmi_acg.pl: Generalized the method of scanning tokens from internal state 
          registry for extracting specie units and friendlies.
        * To avoid MAPL_UNDEFs in the imported TROPP, now saving the most recent
          valid tropopause pressures in w_c%qa(iT2M)%data3d(:,:,km), and no longer
          invoking Chem_UtilTroppFixer.

2012-08-15 <jon.e.nielsen@nasa.gov> Tag: Ganymed-1_0_UNSTABLE_JEN-m4
        * Enable volume mixing ratio tendency as a unit for GMI's diagnostic
          emissions export states whose names begin with EM_.  Included is the name
          change to EM_LGTNO for both prescribed and parameterized lightning NO.
        * MOIST and TURB tendencies added to gmi_acg.pl.  Note: PHYSICS myName
          changed to iName for IM and IT pointers.

2012-08-10 <jon.e.nielsen@nasa.gov> Tag: Ganymed-1_0_UNSTABLE_JEN-m4
        * Export states for total ozone (GMITO3) and tropospheric total ozone (GMITTO3).
        * Emission species (Soot, NO, CO, ... , CH4) export states to KM levels.

2012-07-23 <jon.e.nielsen@nasa.gov> Tag: Ganymed-1_0_UNSTABLE_JEN-m4
        * Set do_smv_reord = F in GMI_GridComp.rc for performance.
        * Explicitly set soil_pulse = 0 in InitializeEmission to avoid floating error that
          first appeared in 2.5x2 Ganymed runs, but in neither 1.25x1 nor 540x90!

2012-05-25 <jon.e.nielsen@nasa.gov> Tag: Ganymed-1_0_UNSTABLE_JEN-m3
        * Brought Fortuna-2_5_b1_JEN species tendencies due to PHYSICS and SUPERDYNAMICS
          into the GNUmakefile and the gmi_acg.pl.

2012-05-24 <jon.e.nielsen@nasa.gov> Tag: Ganymed-1_0_UNSTABLE_JEN-m2
        * KBLOOP parameters in smv2chem_par.h set to 32 for performance on Westmere nodes.

2012-04-24 <jon.e.nielsen@nasa.gov> Tag: Ganymed-1_0_UNSTABLE_JEN-m1
        * Removed obsolete code in GmiChemistry and GmiEmission to help compilation.
        * GMI_GridComp.rc file definitions to ExtData.

2012-03-07 <jon.e.nielsen@nasa.gov> Tag: Ganymed-1_0_UNSTABLE_JEN
        * First GMIchem runs using FV-cubed.
	* Incorporated J. Kouatchou's seven GridComp class modules, with modifications,
          at the GMI level. 
	* Grid information passed to the GridComp classes from ESMF Grid at the
          GMIchem level, rather than using w_c%grid.
        * Chemical tendencies now handled with ESMF bundles, which associated changes
          to the automatic code generator, gmi_acg.pl.  Export state names now are like
          CH4_GMIINC. Species tendencies due to PHYSICS and SUPERDYNAMICS not yet included.
        * Fast JX version 6.5 added to GmiChemistry photolysis for future use. fixed_const
          changed to one time level and fixed_const_timpyr eliminated.
	* Parameterized lightning-generated NO is included.

2012-02-16 <jon.e.nielsen@nasa.gov> Tag: Fortuna-2_5_b1_JEN
        * Moved GMI chemical increments (tendencies) to BUNDLE, which eliminates
	  need for DQGMI_GetPointer___.h and DQGMI_FillPointer___.h files.
	* Added functionality in AGCM and PHYSICS to compute and export the
	  increments (tendencies) due to SUPERDYNAMICS (advection) and physical
	  processes (chemistry excepted).
	* Modified gmi_acg.pl to generate two include files (each) for AGCM and
	  PHYSICS that enable the respective increments to be calculated only 
	  for the GMI species friendly to DYNAMICS (Q4AGE through HNO3COND), 
	  without touching the first 7 FIELDS in the TRADV bundle.
	* Removed the independent calculation of H2OCOND mixing ratio in condense.F90
          to enforce uniformity with QCTOT, which is imported from MOIST.
        * Fill export state for SAD ice effective radius (REFFICE).
	* Changed age of air to AOADAYS, and now uses same algorithm as PCHEM.
	* Parameterized lightning flash rates imported from MOIST, and lightning-generated
          NO is provided by GmiEmission/lightning/GmiEmissionLightning_mod.F90

2011-12-13 <jon.e.nielsen@nasa.gov> HEAD
        * Update StratChem to (1) JPL 2011 and (2) disallow any changes
          to H2O and H2OCOND based on internal microphysics (SUBROUTINEs
	  pscs and sediment).

2011-09-21 <jon.e.nielsen@nasa.gov> Tag: Hypatia-1_0_UNSTABLE_JEN
        * Generalized the connectivities between GMICHEM and GOCART 
	  to support those cases in which fewer than all five GOCART 
	  dust/aerosol classes are being imported to GMICHEM. Also allows
	  GMICHEM to be run in tandem with, for example, GOCART::Rn.
	* Updates to gmi_acg.pl for units and for filling DD and WD export 
	  states.
	* SC: Fill export O3.

2011-07-06 <jon.e.nielsen@nasa.gov>
        * GMICHEM: New functionality added to gmi_acg.pl that adds export states
	  for species tendencies due to chemistry. Compiled and tested in 
	  Fortuna-2_4_BETA2 and put on HEAD.  Pushed tag: Fortuna-2_4_BETA2_JEN.

2011-05-25 <jon.e.nielsen@nasa.gov>
        * GMICHEM: New functionality added to gmi_acg.pl that adds export states
	  for reaction rates constants and rates generated by chem_update.F90.   
	  Compiled and tested in Fortuna-2_4_BETA2 and put on HEAD.

2011-04-29 <jon.e.nielsen@nasa.gov>
        * GMICHEM: New gmi_acg.pl, along with mapl_acg.pl, are run in a three-
          step process to generate code fragments for declaring and getting
          pointers and filling some export states.  Scavenging and deposition
          export specs have been added for several species, in addition to HBr 
          (see entry immediately below).  Tested in Fortuna-2_4_BETA1 and 
          compiled in BETA_2, and put on HEAD.

2011-04-12 <jon.e.nielsen@nasa.gov>
        * GOCART: CO and CO2 rc changes from 2011-03-18 propagated to CMIP and PIESA.
	* GMICHEM: Inserted Henry's Law constants for HBr in setkin_depos.h.

2011-03-30 <jon.e.nielsen@nasa.gov> STRATCHEM updates:
        * Import A-grid cell area from DYN, making SUBROUTINE setmcor obsolete.
	* Added capability to set lightning NOx source magnitude in SC_GridComp.rc.
	* Maximum solar zenith angle for daylight computations now parsed from 
          SC_GridComp.rc.  Code and tables work up to 94 degrees.
        * Added Chapman functions to meso_phot.F.
	* Grab new xtab file from Randy Kawa that fixes NO3 photolysis rate.
	* Use h2oc from SUBROUTINE pscs instead of QCTOT when sedimenting NAT.
        * Merged and compiled with Fortuna-2_4_UNSTABLE and put on HEAD.

2011-03-18 <jon.e.nielsen@nasa.gov>
        * Removed the GEOS-4 references in CO2.
        * Rewrote the PBL partitioning for biomass burning emissions in
	  both CO and CO2, using ZLE (instead of pressure) to get layer 
	  depths and compare with ZPBL.  Not zero diff.
	* Moved CO emission amplification factors ff, bf, bb to RC file.
        * Merged with Fortuna-2_4_BETA1 and put on HEAD.


