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 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
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 emissions, deposition, species, chemistry) 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 the following link for complete information about the validation of GEOS-Chem v11-02b:

  1. Approval form for 1-month benchmark simulation v11-02b
Feature Submitted by Type Status
Features not affecting the full-chemistry simulation:
Source code updates for compatibility with GCHP v1.0.0 GCHP development team Structural In progress
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

Feature Submitted by Type Status
Features affecting the full-chemistry simulation:
Updates to isoprene chemistry, includes:
  • Fast photolysis of carbonyl nitrates
  • Aerosol uptake of organic nitrates
  • Updated organic deposition
  • Remove dependence of species drydep on HNO3 drydep
 Jenny Fisher (U. Wollongong)
Eloïse Marais (Harvard)
Kelvin Bates (Caltech)
Katie Travis (Harvard)
Rebecca Schwantes(Caltech) 		Science
  • Delivered to GCST (Mar 2017)
Enhance default GEOS-Chem simple SOA Sal Farina (Colorado State)
Aerosols Working Group Chairs 		Science
  • Completed Apr 2017
Add aqueous isoprene uptake to SOA scheme Eloise Marais (Harvard) Science
  • Delivered to GCST (Jul 2016)


Carbon balance (fix C creation) Sarah Safieddine (MIT) Bug fix
Features not affecting the full-chemistry simulation:
HEMCO updates: Christoph Keller (NASA GMAO)
Andy Jacobson (NOAA) 		Structural
  • Delivered to GCST (May 2017)
Bug fixes for the ND50 timeseries diagnostic Chris Holmes (Florida State) Bug fix
  • Completed 13 Apr 2017
Fixed an incorrect format statement in input_mod.F Chris Holmes (Florida State) Bug fix
  • Completed 18 Apr 2017
Fix STE fluxes and add to benchmark procedure GCST Bug fix

v11-02d

Feature Submitted by Type Status
Features affecting the full-chemistry simulation:
Halogen chemistry updates Tomás Sherwen (York)
Johan Schmidt (Harvard)
Oxidants and Chemistry WG 		Science
Sulfur oxidation by reactive halogens Qianjie Chen (UW) Science
Features not affecting the full-chemistry simulation:
TBD

v11-02e

Feature Submitted by Type Status
Features affecting the full-chemistry simulation:
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)
Metal catalyzed oxidation of SO2 (as a switch) Becky Alexander (UW) Science
Features not affecting the full-chemistry simulation:
Radon flux diagnostic Benchmark GCST

In the pipeline

Feature Submitted by Type Status


On hold
Compile with PRECISION=4 as the default–declare most real variables as REAL*4 instead of REAL*8 GCST Structural
  • Code is already in place, awaiting activation
  • NOTE: this option may result in less optimal mass conservation than with PRECISION=8, so at this time we will leave it as an option rather than as a standard feature.
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
Transport updates
GEOS resolution & subgrid convection Karen Yu (Harvard) Science
Emissions updates
OMI-based Volcanic emissions 2005-2012 Jun Wang (U. Iowa) Science
  • Delivered to Christoph Keller?
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
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
  • 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
Global ethane emissions Zitely Tzompa (CSU) Science
Inefficient combustion emissions in Africa (DICE-Africa inventory) Eloise Marais (U. Birmingham)
Christine Wiedinmyer (NCAR) 		Science
Trash burning emissions Eloise Marais (U. Birmingham)
Christine Wiedinmyer (NCAR) 		Science
GFAS biomass burning emissions Mat Evans (York) Science
MEIC emissions over China Jonathan Moch (Harvard), Loretta Mickley (Harvard) Science
Anthropogenic PM2.5 dust source Sajeev Philip (Dalhousie) Science
  • Delivered to GCST (Mar 2017)
Deposition/surface updates
Harmonizing Henry's Law coefficients across wet and dry deposition GCST Science
Sedimentation of stratospheric aerosols Sebastian Eastham (Harvard) Science
Wet scavenging in mixed-phase clouds Bo Zhang (NIA/NASA Langley) Science
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
India nested-grid for GEOS-5 Sreleekha Chaliyakunnel (U. Minnesota) Science
Africa nested-grid for GEOS-5 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
Arsenic simulation Shiliang Wu (MT) Science
Structural updates
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 3a: Output diagnostics in NetCDF format GCST Structural
NetCDF Output Phase 3b: Updates to eliminate differences between single and multi-segmented GEOS-Chem runs GCST
Christoph Keller 		Bug fix/Structural
Expansion of model capabilities
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
FlexGrid: Use HEMCO I/O and regridding capabilities to read and regrid met fields 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
Archival of roughness length for temperature z0T GCST Met processing

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/

--Melissa Sulprizio (talk) 22:21, 29 March 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
TBD TBD

Previous issues now resolved in GEOS-Chem v11-02

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

Fixed an incorrect format statement in input_mod.F

This update will be added to v11-02c.

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

These issues will be resolved in GEOS-Chem v11-02c.

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)

Removed the NNPAR parameter from CMN_SIZE_mod.F

This update will be added to v11-02a.

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 will be added to v11-02a.

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 update will be added to v11-02a.

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 will be added to v11-02b.

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 will be added to v11-02b.

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.

        ! 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 will be added to v11-02b.

A pressure update was introduced in v11-01h that corrected an advection issue in which tracer mass was transported relative to moist rather than dry air. To conserve mass throughout the model, all unit conversions were updated to use a dry pressure difference consistent with the new values used in advection. This replaced the previous method which calculated dry pressure difference per level directly from moist edge pressures and GMAO specific humidity.

Meemong Lee discovered that a CO2-only unit conversion for carbon dioxide emissions in co2_mod.F continued to use an old method for converting units that pre-dated the v11-01h update. To correct this, the unit conversion should be changed to be consistent with the analogous unit conversion in unitconv_mod.F90.

Prior to fix: 

              E_CO2  =  HcoState%Spc(IDff)%Emis%Val(I,J,1)
    &                * DTSRCE / ( State_Met%DELP(I,J,1) 
    &                * G0_100 * ( 1.0e+0_fp
    &                - State_Met%SPHU(I,J,1) * 1.0e-3_fp ) )

Update: 

            E_CO2  =  HcoState%Spc(IDff)%Emis%Val(I,J,1)
    &                * DTSRCE * ( 1.0e+0_fp / ( g0_100
    &                * State_Met%DELP_DRY(I,J,L) ) )

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

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

TBD

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