GEOS-Chem v11-02

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Overview

History

The table below shows the previous, current, and successive versions of GEOS-Chem:

Previous version This version Next version
GEOS-Chem v11-01 GEOS-Chem v11-02 TBD
PUBLIC RELEASE 01 Feb 2017 TBD TBD
View v11-01 benchmark history View v11-02 benchmark history TBD

What's new in this version

NOTE: v11-02a, v11-02b, etc. denote 1-month benchmark simulations, which are designed to evaluate GEOS-Chem's performance at intermediate stages of development.

v11-02a

Please see the following link for complete information about the validation of GEOS-Chem v11-02a:

  1. Approval form for 1-month benchmark simulation v11-02a
  2. Results for 1-year benchmark simulation v11-02a-Run0
  3. Results for 1-year benchmark simulation v11-02a-Run1 (final version)
Feature Submitted by Type Status
Features affecting the full-chemistry simulation:
Update chemistry rate constants based on JPL Publication 15-10 Barron Henderson (US EPA),
Mat Evans (U. York), &
Oxidants and Chemistry WG
Science Approved 12 May 2017
Fixes to correct ALK4 lumping issue Barron Henderson (US EPA) Science " "
PAN updates, including:
  • Updates to emissions, deposition, species, chemistry
  • Ocean+biogenic ALD2 emissions from Millet al. [2010]
Emily Fischer (CSU) Science " "
Monthly mean NEI2011 emissions GCST &
Katie Travis (Harvard)
Science " "
Bug fixes in the GEOS-Chem sulfate module:
Prasad Kasibhatla (Duke)
Prasad Kasibhatla (Duke)
Qianjie Chen (UW)
Viral Shah (UW)
Bug fix " "
Fix bug in dry deposition aerodynamic resistance Brian Boys (Dalhousie) Bug fix " "
Fix acetone parameterization in hcox_seaflux_mod.F90 GCST Bug fix " "
Bug fix in cos(SZA) for start of timestep Lizzie Lundgren (GCST) Bug fix " "
Include TOA pressure when calculating dry pressure edges Seb Eastham (Harvard) Science " "
Features not affecting the full-chemistry simulation:
Implement ISORROPIA v2.0 as a Fortran module Seb Eastham (Harvard) &
GCST
Structural " "
Updates to the HEMCO emissions component:
Christoph Keller (NASA GMAO)
Seb Eastham (Harvard)
Jessica Morena (Dalhousie)
Brian Boys (Dalhousie) & GCST
Structural
& Bug fix
" "
Updates to gain computational speedup:
Mike Long (Harvard)
Bob Yantosca (GCST)
Structural
& Bug fix
" "
Fixed typo in INIT_WINDOW Bob Yantosca (GCST) Bug fix " "
netCDF file I/O updates:
Chris Holmes (Florida State)
Andy Jacobson (NOAA)
GCST
Bug fix &
Structural
" "
Makefile and build sequence updates:
Jiawei Zhang (Harvard)
GCST
Bug fix &
Structural
" "
Bug fixes for running UCX in ESMF environment Christoph Keller (NASA GMAO) Bug fix " "
Bug fixes for diagnostics:
Aaron van Donkelaar (Dalhousie)
Jenny Fisher (U. Wollongong)
GCST
Jenny Fisher (U. Wollongong)
Chris Holmes (Florida State)
Bug fix " "
Removal of obsolete variables: GCST Structural " "

v11-02b

Please see the following link for complete information about the validation of GEOS-Chem v11-02b:

  1. Approval form for 1-month benchmark simulation v11-02b
  2. Approval form for 1-month benchmark simulation v11-02b with high performance option (v11-02b-HP)
  3. Results for 1-year standard benchmark simulation of v11-02b-HP Run0
  4. Results for 1-year standard benchmark simulation of v11-02b-HP Run1 (uses offline archived lightning and dust emissions)
  5. Results for 1-year RnPbBe benchmark simulation of v11-02b-HP
Feature Submitted by Type Status
Features not affecting the full-chemistry simulation:
Source code updates for high performance option (GCHP) Seb Eastham (Harvard)
Lizzie Lundgren (Harvard)
Mike Long (Harvard)
Jiawei Zhuang (Harvard)
Bob Yantosca (Harvard)
Structural Approved 16 Jun 2017
Bug fixes for diagnostics:
Ilya Stanevic (Toronto)
Lee Murray (Rochester)
Bug fix " "
Write initial and final Ox mass to file when using the tagged O3 simulation Bob Yantosca (GCST) Structural " "
Convert CO2 emissions units using dry pressure used in advection Meemong Lee (JPL) Science " "
Add QFED emissions for 2014-2016 Christoph Keller (NASA GMAO) Science " "

v11-02c

Please see the following link for complete information about the validation of GEOS-Chem v11-02c:

  1. Approval form for 1-month benchmark simulation v11-02c
  2. Results for 1-year benchmark simulation v11-02c-Run0
Feature Submitted by Type Status
Features affecting the full-chemistry simulation:
Enhance default GEOS-Chem simple SOA Sal Farina (Colorado State)
Aerosols Working Group Chairs
Science 1-month benchmark:
Approved on 07 Sep 2017

1-year benchmark:
Approved 21 Sep 2017

Updates to isoprene and monoterpene chemistry Katie Travis (MIT)
Jenny Fisher (U. Wollongong)
Eloïse Marais (U. Birmingham)
Christopher Chan Miller (Harvard)
Kelvin Bates (Caltech)
Rebecca Schwantes(Caltech)
Science " "
Add aqueous isoprene uptake to SOA scheme Eloise Marais (U. Birmingham) Science " "
Carbon balance (fix C creation) Sarah Safieddine (MIT) Bug fix " "
Fix bugs for EOH and MGLY following implementation of PAN updates in v11-02a Melissa Sulprizio (GCST) Bug fix " "
Update HEMCO from v2.0.004 to v2.1.001 Christoph Keller (NASA GMAO) Structural " "
Features not affecting the full-chemistry simulation:
HEMCO updates:
Christoph Keller (NASA GMAO)
Andy Jacobson (NOAA)
Paulo Tuccella (L'Aquila)
Structural " "
Fixes for several minor issues:
Chris Holmes (Florida State)
Chris Holmes (Florida State)
Jiawei Zhuang (Harvard)
Amanda Giang (MIT)
Katie Travis (MIT)
Katie Travis(MIT)
Bug fix " "
Fixes for the TOMAS simulation:
Sal Farina (Colorado State)
Jack Kodros (Colorado State)
Bob Yantosca (GCST)
Bug fix " "
Fix STE flux diagnostics and add to benchmark procedure Melissa Sulprizio (GCST) Bug fix &
Benchmarking
" "
Initial structural modifications for netCDF diagnostics:
  • Introduce Headers/State_Diag as a stub module (for now)
  • Add a registry object into State_Met, State_Diag, and State_Chm in order to obtain a pointer to any module variable (or slice) by looking up its name
  • Add new module Headers/registry_mod.F90 which contains derived types and routines for registering module variables.
Bob Yantosca (GCST) Structural " "
Combine timestep settings in input.geos in a Timesteps menu Melissa Sulprizio (GCST) Structural " "
Update CO data used in 1-year benchmark plots Jenny Fisher (U. Wollongong) Benchmarking " "

v11-02d

Feature Submitted by Type Status
Features affecting the full-chemistry simulation:
Halogen chemistry updates Tomás Sherwen (York)
Johan Schmidt (Harvard)
Seb Eastham (MIT)
Lei Zhu (Harvard)
Oxidants and Chemistry WG
Science Under evaluation
Sulfur oxidation by reactive halogens Qianjie Chen (UW) Science
Add bug fixes for GLYX, MGLY, IEPOX, and IMAE heterogeneous chemistry Sebastian Eastham (MIT) Bug fix
Features not affecting the full-chemistry simulation:
Update CH4 latitude bands for 2014-2016 Katie Travis (MIT) Science
Remove support for GCAP, GEOS-4, MERRA, GEOS-5 Melissa Sulprizio (GCST) Structural
Timestamp HEMCO diagnostics filename with start time rather than end time Lizzie Lundgren (GCST) Structural
Structural updates for netCDF diagnostics GCST Structural

v11-02e

Feature Submitted by Type Status
Features affecting the full-chemistry simulation:
Sync GEOS-FP files on Harvard ftp with files at Dalhousie GCST Bug fix
Update density of BC to 1.8 and add absorption enhancement factor in input.geos Xuan Wang (MIT) Science
  • Delivered to GCST (Jan 2016)
Monthly mean surface methane distributions Lee Murray (NASA GISS/LDEO) Science
Remove initial stratospheric 2D mixing ratio option Seb Eastham (Harvard) Science
UCX stratospheric water boundary condition update Chris Holmes (UC Irvine)
Seb Eastham (Harvard)
Science
  • Delivered to GCST (Jan 2017)
Use monthly mean stratospheric prod/loss rates from UCX simulation for all species GCST Science
  • Delivered to GCST (Nov 2017)
Metal catalyzed oxidation of SO2 (as a switch) Viral Shah (UW)
Becky Alexander (UW)
Science
Spatially varying OM/OC Sajeev Philip (Dalhousie/NASA Ames) Science
  • Delivered to GCST (May 2017)
Add bug fixes for aerosols Jingyuan Shao (UW) Bug fix
  • Delivered to GCST (Nov 2017)
Remove MONX from chemical mechanisms Sam Silva (MIT) Bug fix
  • Delivered to GCST (Nov 2017)
Features not affecting the full-chemistry simulation:
Diagnostic for correcting ozone from the height of the lowest model level to the surface Structural Katie Travis (MIT)
  • Delivered to GCST (Nov 2017)

In the pipeline

Feature Submitted by Type Status
Transport updates
GEOS resolution & subgrid convection Karen Yu (Harvard) Science
  • Delivered to GCST (Oct 2017)
Emissions updates
Use global 0.25x0.25 files for MEGAN input and MODIS LAI Jenny Fisher (U. Wollongong)
Eloise Marais (U. Birmingham)
Dylan Millet (UMN)
Bug fix/
Science
  • Delivered to GCST (Nov 2017)
Update to HEMCO v2.1.003 (requires updated MODIS LAI data) Christoph Keller (NASA GMAO) Structural
  • Delivered to GCST (Jul 2017)
OMI-based Volcanic emissions 2005-2012 Jun Wang (U. Iowa) Science
EDGAR v4.3.1 emissions Chi Li (Dalhousie) Science
  • Delivered to GCST (Nov 2016)
EPA-derived BC/OA emissions over US (1990-2012) David Ridley (MIT)
Chi Li (Dalhousie)
Science
  • Need to coordinate between Ridley and Li versions
Historical CAC emissions Chi Li (Dalhousie) Science
  • Delivered to GCST (Nov 2016)
Ammonia emissions from Arctic seabirds Betty Croft (Dalhousie) Science
  • Delivered to GCST (Nov 2017)
Ocean ammonia emission inventory Fabien Paulot (NOAA/GFDL) Science
  • Data files delivered to GCST (Jan 2016)
  • Needs to be implemented via HEMCO
A snow NOx source from deep snowpack Maria Zatko (UW)
Becky Alexander (UW)
Science
  • Delivered to GCST (Nov 2017)
  • Implemented in v9-01-01
  • Needs to be added as a HEMCO extension
MASAGE inventory in HEMCO as default Fabien Paulot (NOAA/GFDL)
Amos Tai (CUHK)
Science
Non-agricultural NH3 for use with MASAGE Amos Tai (CUHK) Science
Radon emission update Bo Zhang (NIA/NASA Langley) Science
  • Files and code updates are ready. Delivery to GCST is pending manuscript submission.
Global ethane emissions Zitely Tzompa-Sosa (CSU) Science
  • Delivered to GCST (May 2017)
Inefficient combustion emissions in Africa (DICE-Africa inventory) Eloise Marais (U. Birmingham)
Christine Wiedinmyer (NCAR)
Science
  • Delivered to GCST (Nov 2017)
Trash burning emissions Eloise Marais (U. Birmingham)
Christine Wiedinmyer (NCAR)
Science
GFAS biomass burning emissions Mat Evans (York) Science
Retire GFED3 biomass burning emissions GCST Structural
MEIC emissions over China (2000-2015) Lu Shen (Harvard)
Melissa Sulprizio (Harvard)
Science
  • Delivered to GCST (Nov 2017)
CEDS global anthropogenic emissions (1950-2014) Lu Shen (Harvard)
Melissa Sulprizio (Harvard)
Science
  • Delivered to GCST (Nov 2017)
Anthropogenic PM2.5 dust source Sajeev Philip (Dalhousie) Science
  • Delivered to GCST (Mar 2017)
FINN biomass burning emissions for 2015-2016 Barron Henderson (US EPA) Science
  • Delivered to GCST (Nov 2017)
Deposition/surface updates
Wet scavenging in mixed-phase clouds Bo Zhang (NIA/NASA Langley) Science
  • Code updates are ready. Delivery to GCST is pending manuscript submission.
Specialty simulation updates
Oxidant fields from v10 for 2006-2012
  • 3D chemical source for CO2, CO
  • OH for tagged CO & CH4
Dylan Jones (UofT) Science
  • Will make data files available on ftp site
Updated Tagged CO simulation Jenny Fisher (Wollongong) Science
  • Delivered to GCST (Nov 2017)
Updated CH4 simulation Bram Maasakkers (Harvard)
Melissa Sulprizio (Harvard)
Science
  • Delivered to GCST (Oct 2017)
India nested-grid for GEOS-5 Sreleekha Chaliyakunnel (U. Minnesota) Science
Africa nested-grid for GEOS-FP and MERRA-2 Eloise Marais (U. Birmingham) Science
West Africa nested-grid for GEOS-FP Mat Evans (York)
Eleanor Morris (York)
Science
Tagged sulfate simulation Becky Alexander (UW) Science
Sea salt aerosol alkalinity Becky Alexander (UW) Science
  • Delivered to GCST (Nov 2017)
Arsenic simulation Shiliang Wu (MT) Science
Structural updates
Updated flux diagnostics Chris Holmes (Florida State)
GCST
Structural/
Benchmarking
NetCDF Output Phase 3a: Output diagnostics in NetCDF format GCST Structural
Expansion of model capabilities
FlexGrid: Use HEMCO to read met fields and enable nested simulations over any custom domains Jiawei Zhuang (Harvard)
Jintai Lin (PKU)
Structural
  • Delivered to GCST (Oct 2016)
Update ISORROPIA from v2.0 to v2.2, in order to remove persistent noise in output Seb Eastham (Harvard) Science
  • Delivered to GCST (May 2017)
Archival of roughness length for temperature z0T GCST Met processing

Defer to v11-03 unless ready in time for v11-02

Item Author(s) Type Status
Mercury updates
Updates to Hg chemistry from Horowitz et al. (2017) Hannah Horowitz (U. Washington)
Colin Thackray (Harvard)
Rebecca Stern (Harvard)
Science
Year 2010 ocean Hg boundary conditions from ocean model Hannah Horowitz (Harvard) Science
Historical products emissions from Zhang et al. (2016), should become default Colin Thackray (Harvard) Science
AMAP/UNEP 2035 for Hg simulation Helene Angot (MIT) Science
Deposition/surface updates
Harmonizing Henry's Law coefficients across wet and dry deposition GCST Science
Sedimentation of stratospheric aerosols Sebastian Eastham (Harvard) Science
Aerosol updates
VBS SOA option Rokjin Park (SNU) Science
Structural updates
Additional modifications for FlexChem, including:
  • Rebuild the pre-built chemistry mechanisms (Standard, Tropchem, UCX, SOA, SOA-SVPOA) with Kppa
  • Add capability for custom chemistry mechanism by building KPP on-the-fly in GEOS-Chem
Mike Long (Harvard)
GCST
Structural
Benchmark of stratospheric simulation Dylan Jones (U. Toronto) Benchmarking
  • 1-yr benchmarks for GEOS-Chem v11-01d and later include comparisons with OSIRIS O3
  • Waiting on OSIRIS NO2 data
  • Waiting on comparisons with ACE-FTS data
Uniformity of units GCST Structural
  • Phase 2 (unit uniformity throughout chemistry) to be implemented after Flexchem
  • Phase 3 (unit uniformity in some specialty simulations) will be implemented in pieces with input from 3rd party developers
  • Phase 4 (removal of area and area-dependent State_Met variables) will be ongoing
ObsPack diagnostic as netCDF replacement for planeflight_mod.F Andy Jacobson (NOAA/ESRL) Structural
  • Delivered to GCST (May 2017)
NetCDF Output Phase 3b: Updates to eliminate differences between single and multi-segmented GEOS-Chem runs GCST
Christoph Keller
Bug fix/Structural

New data directories

The following HEMCO data directories have been added or updated for GEOS-Chem v11-02. You will have to download the directories relevant to your simulation.

Inventory What was added? When added? Directory
NEI2011 North American emissions Monthly mean data files (created from the existing hourly data in HEMCO/NEI2011/v2015-03) v11-02a HEMCO/NEI2011/v2017-02-MM/
ALD2 Fields for ALD2 emissions, including:
  • Seawater concentration of acetaldehyde
  • Heterotrophic respiration rates, used to compute biogenic emissions of ALD2 and EOH

(added with the PAN updates)

v11-02a HEMCO/ALD2/v2017-03/
POET Anthropogenic emissions of ethanol from the POET inventory
(added with the PAN updates)
v11-02a HEMCO/POET/v2017-03/
Soil NOx New file: DepReservoirDefault.nc
Read default DEP_RESERVOIR fields from file when not found in HEMCO restart file
v11-02a HEMCO/SOILNOX/v2014-07/
QFED Data for 2014-2016 v11-02b HEMCO/QFED/v2014-09/

--Melissa Sulprizio (talk) 21:49, 22 May 2017 (UTC)

Validation

In this section we provide information about the benchmarks and tests that we have done to validate GEOS-Chem v11-01.

1-month and 1-year benchmarks

For complete information about the benchmark simulations used to validate GEOS-Chem v11-02, please see our GEOS-Chem v11-02 benchmark history wiki page.

Unit tests for GEOS-Chem v11-02

We perform a full set of unit tests on GEOS-Chem on an almost daily basis. These tests ensure that each new feature being added does not break any existing functionality.

Here are the unit tests that we ran before submitting 1-month benchmark simulation for v11-02. Click on the links below to see the results from each set of unit tests:

Unit test Date
v11-02a 17 Apr 2017
v11-02b 18 May 2017

Previous issues now resolved in GEOS-Chem v11-02

The following bugs and/or technical issues have been resolved in v11-02:

Removed the NNPAR parameter from CMN_SIZE_mod.F

This update was included in v11-02a and approved on 12 May 2017.

The NNPAR parameter is a holdover from when we used COMMON blocks to store GEOS-Chem arrays. With the advent of the GEOS-Chem species database, we now use State_Chm%nSpecies to represent the total number of species in the chemistry mechanism, and State_Chm%nAdvect to represent the total number of advected species.

We have therefore removed the following lines (in RED) from CMN_SIZE_mod.F:

      !=================================================================
      ! TRACER & EMISSION SPECIES PARAMETERS
      !
      ! NNPAR   = max number of tracers
      ! NEMPARA = max number of anthropogenic emission species
      ! NEMPARB = max number of biogenic      emission species
      !=================================================================
      ! increase NNPAR and NEMPARA an extra amount (hotp 7/31/09)
#if   defined( TOMAS )
# if    defined( TOMAS40 )
      INTEGER,    PARAMETER :: NNPAR   = 430   ! For TOMAS40 (sfarina 6/11/13)
# elif  defined( TOMAS15 )
      INTEGER,    PARAMETER :: NNPAR   = 205   ! For TOMAS15 (sfarina 6/11/13)
# elif  defined( TOMAS12 )
      INTEGER,    PARAMETER :: NNPAR   = 178   ! For TOMAS12 (sfarina 6/11/13)
# else
      INTEGER,    PARAMETER :: NNPAR   = 340   ! For TOMAS (win, bmy, sfarina 6/11/13)f
# endif
#else
      INTEGER,    PARAMETER :: NNPAR   = 150   ! For non-TOMAS simulations
#endif

--Bob Yantosca (talk) 20:27, 17 March 2017 (UTC)

Print the version number to the log file

This update was included in v11-02a and approved on 12 May 2017.

In routine DISPLAY_GRID_AND_MODEL of GeosCore/main.F, we now print out the version number, e.g.

Using GEOS-Chem version: v11-02

to the log file (i.e. stdout output stream). This will facilitate debugging.

--Bob Yantosca (talk) 18:21, 16 March 2017 (UTC)

Include TOA pressure when calculating dry pressure edges

This fix was included in v11-02a and approved on 12 May 2017.

For physicality and consistency with GCHP, the top-of-atmosphere (TOA) pressure is now included when calculating dry pressure edges. The following lines in GeosCore/dao_mod.F were changed from:

     ! Reset dry surface pressure to zero
     PS_DRY = 0.0e+0_fp

to:

     ! Reset dry surface pressure to TOA value
     PS_DRY = GET_AP(LLPAR+1)

--Melissa Sulprizio (talk) 20:47, 14 April 2017 (UTC)

ND26 vertical flux diagnostic does not yield mass balance in advection

This update was included in v11-02b and approved on 16 Jun 2017.

To achieve mass balance in the advection diagnostic output (ND24, ND25, and ND26) Ilya Stanevic (U. Toronto) suggested that the FZ array be used to compute the ND26 vertical mass flux diagnostic for all levels. This is similar to how FX is used for ND24 and FY for ND25. Note that this fix is only for global advection since the FZ array is not defined for the nested model. With this update, the global ND26 vertical flux diagnostic is defined as the flux into the grid box above (e.g. ND26(:,:,1) is flux from level 1 to level 2 and ND26(:,:,LLPAR) is all zeros).

--Lizzie Lundgren (talk) 21:41, 9 May 2017 (UTC)

ND40 planeflight diagnostic not always written out when turned on

This update was included in v11-02b and approved on 16 Jun 2017.

Lee Murray (University of Rochester) wrote:

I think the FlexChem implementation accidentally disabled the planeflight diagnostic for the full chemistry simulation. We used to initialize the planeflight diagnostic in chemdr.F for full chemistry simulations (now no more) and all the other versions in main.F. We should change main.F to always call SETUP_PLANEFLIGHT whenever the diagnostic is turned on (remove code in RED, add code in GREEN).
        ! Plane following diagnostic
        IF ( ND40 > 0 .and. DO_DIAG_WRITE ) THEN 
        
           ! Call SETUP_PLANEFLIGHT routine if necessary
           IF ( ITS_A_NEW_DAY() ) THEN
              
!               ! If it's a full-chemistry simulation but LCHEM=F,
!               ! or if it's an offline simulation, call setup routine 
!               IF ( ITS_A_FULLCHEM_SIM ) THEN
!                  IF ( .not. LCHEM ) THEN
!                     CALL SETUP_PLANEFLIGHT( am_I_Root, Input_Opt,
!     &                                       State_Chm, RC )
!                  ENDIF
!               ELSE
!                  CALL SETUP_PLANEFLIGHT( am_I_Root, Input_Opt, 
!     &                                    State_Chm, RC )
!               ENDIF

               CALL SETUP_PLANEFLIGHT( am_I_Root, Input_Opt, State_Chm, RC )

           ENDIF
        ENDIF

--Lizzie Lundgren (talk) 19:44, 10 May 2017 (UTC)

CO2 emissions unit conversion not consistent with new advection pressure

This update was included in v11-02b and approved on 16 Jun 2017.

We have moved the discussion of this issue to our CO2 simulation wiki page.

--Lizzie Lundgren (talk) 19:44, 10 May 2017 (UTC)

Fixed an incorrect format statement in input_mod.F

This update was included in v11-02c and approved on 21 Sep 2017.

Chris Holmes wrote:

An incorrect format specification caused GEOS-Chem to crash rather than write a helpful error message when the transport timestep is too big. The code in RED was removed and the lines in GREEN was added at approximately line 3324 of input_mod.F.
        IF ( Input_Opt%TS_DYN > MAX_DYN .and. LTRAN ) THEN
           write(MSG,'(I8,a,L)') '<>', Input_Opt%TS_DYN, Input_Opt%HPC
           WRITE( MSG, 300 ) 'Transport timestep exceeds max:',
    &                         Input_Opt%TS_DYN, MAX_DYN
300        FORMAT( a, i8, ' >', i8 ) 
           CALL ERROR_STOP( MSG, LOCATION )
        ENDIF

--Bob Yantosca (talk) 17:55, 18 April 2017 (UTC)

Bug fixes for the ND50 timeseries diagnostic

This update was included in v11-02c and approved on 21 Sep 2017.

Chris Holmes wrote:

I have found what I suspect are two bugs in ND50.

1. Function ITS_TIME_FOR_WRITE_DIAG50() checks if the integer part of the hour is zero to decide whether to write to disk. With the 20 minute time steps recommended in v11-01, Diag50 gets written and overwritten multiple times in the first hour of every day! The fix is simply to have this function return TRUE if the GMT time is 00:00.

2. Within WRITE_DIAG50 there is the following block of code
        ! Pick the proper divisor, depending on whether or not the
        ! species in question is archived only each chem timestep
        SELECT CASE ( ND50_TRACERS(W) )
           CASE (91, 92, 76, 77 )
              DIVISOR = COUNT_CHEM3D
           CASE DEFAULT
              DIVISOR = COUNT
        END SELECT

I see nothing special about tracers 76, 77, 91, and 92 that should make them divided by a different number. The special tracers numbers are all >= 150 for ND50. I suspect this is left over from a previous code revision. I think it should be DIVISOR=COUNT for all ND50_Tracers.

--Bob Yantosca (talk) 14:42, 14 April 2017 (UTC)

Add MERRA2 to #if and #elif statements where it had been omitted

This update was included in v11-02c and approved on 21 Sep 2017.

Jiawei Zhuang wrote:

In v11-02, (commit 8d27b9a), I am trying to unify defined( GEOS_FP ) and defined( MERRA ) by a adding a new tag defined( FlexGrid ). However, I find some model codes that treat them differently without explanation:
(1) In GeosCore/convection_mod.F: At the #if statement at line 1443, MERRA2 will execute the #else block. But it should execute the #if block:
      #if defined( GEOS_5 ) || defined( GEOS_FP ) || defined( MERRA )
          ! Do nothing, these are all hybrid grids
      #else
          ... etc ...
(2) In HEMCO/Core/hco_interp_mod.F90, MERRA2 will skip the #elif block at line 531:
      #elif defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
          ! Full grid
          ... etc ...
(3) At line 1193 of GeosCore/hcoi_gc_main_mod.F90, I noticed what appears to be a typo:
      #if defined ( GEOS_FP ) || ( MERRA2 )
(4) At line 779 of GeosCore/land_mercury_mod.F, I noticed this #if block, which could be written better:
            IF ( FIRSTTIME ) THEN
      #if !defined( MERRA2 ) || !defined( GEOS_FP )
               WRITE( 6, * ) 'WARNING: Snow emission parameterization '//
         &       'designed for use with incident '
               WRITE( 6, * ) 'shortwave radiation. Only net shortwave '//
         &       'radiation available.'
      #endif
               FIRSTTIME = .FALSE.
           ENDIF
(5) In KPP/Standard/gckpp_HetRates.F90, there are 3 places that seem to miss defined (MERRA2):
      ! continental or marine clouds only...
#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
      IF ( (FRLAND (I,J) > 0) .or. (FROCEAN(I,J) > 0) ) THEN
#else
      ! Above line is to skip over land ice (Greenland and Antartica). This
      ! should do the same (and also work for GEOS-5, but leave above for now).
      IF ( IS_LAND .and. .not. IS_ICE  ) THEN
#endif

#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
      IF ( FRLAND(I,J) > FROCEAN(I,J) ) THEN
#else
      IF ( IS_LAND ) THEN
#endif

#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
      ! QL is [g/g]
      Vc = CLDF(I,J,L) * QL * AD(I,J,L) / dens_h2o
#else
      ! QL is [cm3/cm3]
      Vc = CLDF(I,J,L) * QL * XAIRM3
#endif

These appear to have been oversights. To fix the issues, simply add the code in GREEN to the #if blocks mentioned above:

 At line 1443 of convection_mod.F: 
 #if defined( GEOS_5 ) || defined( GEOS_FP ) || defined( MERRA ) || defined( MERRA2 )

 At line 531 of hco_interp_mod.F90:
 #elif defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
 
 At line 1193 of hcoi_gc_main_mod.F90
 #if defined( GEOS_FP ) || defined( MERRA2 )

 At line 779 of land_mercury_mod.F:
 #if defined( GEOS_FP ) || defined( MERRA2 )
    ! do nothing
 #else
     WRITE( 6, * ) ... etc ...

 At lines 1953, 2029, and 2047 of KPP/Standard/gckpp_HetRates.F90
 #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )

--Bob Yantosca (talk) 20:28, 22 May 2017 (UTC)

Code cleanup suggestions

Suggestion 1 was included in v11-02c and approved on 21 Sep 2017.

Suggestion 2 is slated for inclusion later in GEOS-Chem v11-02.

Chris Holmes wrote:

I have a few housekeeping suggestions that I think would be helpful to GC users.
  1. Combine all of the timestep settings in input.geos in a single “Timesteps” menu. With the default timesteps being much shorter now, there seems to be much more interest in changing these timesteps (e.g. do model development with large time steps, then publication runs with small time steps), myself included. It would be nice to change all of the time steps in one place. Besides making it easier to double or halve them all, a single menu would also help clarify whether the time steps for each process have the recommended 1:2 ratio for operator splitting.
  2. Move all of the photolysis and aerosol optics data files out of the run directory and into a folder in ExtData. That would allow them to be documented, tracked and updated like emissions. As far as I have seen, these files are rarely modified by users, so they don’t need to be in the run directory. That would include the following files...
      brc.dat
      dust.dat
      FJX_j2j.dat
      FJX_spec.dat
      h2so4.dat
      jv_spec_mie.dat
      org.dat
      so4.dat
      soot.dat
      ssa.dat
      ssc.dat

--Melissa Sulprizio (talk) 16:37, 19 July 2017 (UTC)

Update CH4 latitude bands for 2014-2016

This update will be included in v11-02d.

The last year of latitudinal CH4 concentration data (based on CMDL flask observations) was 2013. (Data is provided in 4 latitude bands: 90°S-30°S, 30°S-0°N:, 0°N-30°N, 30°N-90°N.) Katherine Travis has updated the subroutine get_global_ch4.F with additional years of latitudinal CH4 data from 2014 thru 2016.

Lee Murray will provide additional latitudinal CH4 concentration data through present day, once it is available. See this post on our NOx-Ox-HC-aerosol wiki page for more information.

--Melissa Sulprizio (talk) 15:16, 5 September 2017 (UTC)

Add bug fixes for GLYX, MGLY, IEPOX, and IMAE heterogeneous chemistry added in v11-02c

This update will be included in v11-02d.

Sebastian Eastham wrote:

There’s a bug in the v11-02c het rate code. In KPP/Standard/gckpp_HetRates.F90, many of the dedicated routines (e.g. HetIMAE) loop over NAERO. The loop looks like
   Do N=1,NAERO
      ! [Comment]
      If (N==8) Then
         XSTKCF = [number] 
      End If
      If (N == 13) Then
         ADJUSTEDRATE = XAREA(N)*XSTKCF
      Else
         ADJUSTEDRATE = ARSL1K( XAREA(N), XRADI(N), XDENA, XSTKCF, XTEMP, (A**0.5_FP) )
      End If
      Het_IMAE = Het_IMAE + ADJUSTEDRATE
   End Do
The problem here is that every aerosol after aerosol 8 is inheriting the sticking coefficient from aerosol 8. Crucially, this includes SOAS – so the fact that the simple SOA tracer is missing could affect this. GCC is artificially increasing the het rate on all aerosols because of this bug, whereas GCHP is not. Fixing this would be as simple as inserting either XSTKCF = 0.0 or XSTKCF = B at the start of the loop, where I’ve written ! [Comment]. The question of which is correct is really a science question (probably XSTKCF = B, although I’d ask the original authors). However, what’s definitely true is that one of these two options needs to be put in or the result of the calculation will be wrong.
Fixing this bug is likely to change SOA burdens in both GCC and GCHP. In gckpp_HetRates, the following routines are definitely affected:
  • HetGLYX
  • HetMGLY
  • HetIEPOX (forms SOAIE)
  • HetIMAE (forms SOAME)
The other het routines look like they have the correct form (either by a "header" of XSTKCF = B, or because they have an If...ElseIf...Else...End clause that catches all possible values of N and sets XSTKCF accordingly).

The solution is to set XSTKCF = TINY(1e0) where ! [Comment] is in the code snippet above, following what is done in Eloise Marais's version of calcrate.F.

--Melissa Sulprizio (talk) 17:57, 20 September 2017 (UTC)

Remove support for GCAP, GEOS-4, MERRA, GEOS-5

This update will be included in v11-02d.

Daniel Jacob wrote to the GEOS-Chem Steering Committee:

I met today with the GCST and they brought up again the issue of discontinuing support for old met fields (GEOS-4, GEOS-5, MERRA) in GEOS-Chem. They told me that it would benefit the code structurally to stop supporting these old met fields, also that GCHP will not be able to use them since the data are in binary format. We would also reclaim some disk storage, and we would satisfy GMAO who doesn’t like that we’re using these old met fields.
We will discontinue support for the old met fields (MERRA, GEOS-4, GEOS-5) in future model versions BUT we will keep the data archives [at Dalhousie] at least for now.

Loretta Mickley consulted with Lee Murray, Amos Tai, and Jeff Geddes of the Chemistry-Ecosystems-Climate Working Group and wrote:

It looks like we can safely retire the GCAP met fields and #ifdef GCAP sections of the code now. As Lee describes, there are other capabilities in use by the chemistry-climate community that we will eventually implement into standard code.
I believe we currently have GCAP2 met fields stored at Harvard, and these should be maintained. GCAP2 consists of met fields from the GISS ModelE2.1 present-day and future. Lee Murray and Eric Leibensperger created these files, after a lot of work!

--Melissa Sulprizio (talk) 16:11, 2 November 2017 (UTC)

Bug fixes for aerosols in v11-01

These fixes will be included in v11-02e.

Jingyuan Shao (UW) wrote:

When I use GEOS-Chem v11-01, I found two small bugs in the codes.
The first is described in more detail at this post on our ISORROPIA II wiki page.
Second, In aerosol_mod.F(line 2077) from
     ! Mass of hydrophilic aerosol from Mian Chin
     ALLOCATE( WAERSL(IIPAR,JJPAR,LLPAR,NAER), STAT=AS)
     IF ( AS /= 0) CALL ALLOC_ERR( 'WAERSL' )
     DAERSL = 0d0
to
     ! Mass of hydrophilic aerosol from Mian Chin
     ALLOCATE( WAERSL(IIPAR,JJPAR,LLPAR,NAER), STAT=AS)
     IF ( AS /= 0) CALL ALLOC_ERR( 'WAERSL' )
     WAERSL = 0d0

--Melissa Sulprizio (talk) 16:28, 15 November 2017 (UTC)

Remove MONX from chemical mechanisms

This fix will be included in v11-02e.

Sam Silva (MIT) wrote:

I was wondering why there were three monoterpene species in the chemical mechanism: MTPA (lumped alpha pinene), LIMO (lumped limonene) and then MONX (all monoterpenes).
MONX doesn’t play with any of the monoterpene nitrate chemistry, it just is converted into 3 formaldehyde:
   MONX = 3.000CH2O :                          GCARR(1.07E-05, 0.0E+00, 0.0);
It seems like having the MONX group (all monoterpenes) and the speciated lumped monoterpenes is an inconsistency. Ultimately, I’m interested in adding Glyoxal formation from monoterpenes, and it’s not clear to me how to properly do that, given the three different species.
Do you know of a reason why MONX is still in the mechanism?

Melissa Sulprizio responded:

I had a look through the Git history of the globchem.dat file. The MONX -> 3CH2O reaction was originally included in the SOA mechanism. Just prior to the v10-01 public release, the GEOS-Chem Steering Committee requested that we include SOA chemistry in the benchmark simulations. At that time, MONX was made an active species and the MONX -> 3CH2O reaction was added to the globchem.dat file for the benchmark simulations. No other monoterpene chemistry was included in that chemical mechanism at the time.

In v11-02a, we introduced monoterpene chemistry during Emily’s PAN updates. At that time MTPA was introduced. The monoterpene chemistry was further modified and expanded upon in v11-02c following Jenny’s updates originally made for SEAC4RS.

Looking back at Emily’s original PAN updates that she sent to us (based on v9-02h), it looks like MONX is a dead species in globchem.dat and the MONX -> 3CH2O reaction is not included. That may have been an oversight during the PAN updates implementation. Since Emily’s globchem.dat did not include the SOA chemistry by default and our standard/benchmark mechanism did, it wasn’t clear that we should remove the MONX species and reaction. However, if it is a bug to continue including that species in v11-02 since we now have other monoterpene species defined then we can certainly remove MONX.

Emily Fischer responded:

I think we should remove MONX.

--Melissa Sulprizio (talk) 16:28, 15 November 2017 (UTC)

Outstanding issues not yet resolved in GEOS-Chem v11-02

TBD

For a complete list of outstanding issues not yet resolved in GEOS-Chem v11-02 with High Performance option, see the outstanding issues section of the GCHP v11-02 wiki page.