Difference between revisions of "GEOS-Chem v11-02"
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− | |Merge source code updates | + | |Merge [[GEOS-Chem HP|GCHP source code updates]] with GEOS-Chem v11-01a |
|Structural | |Structural | ||
|GCHP development team<br>[[GCST]] | |GCHP development team<br>[[GCST]] |
Revision as of 17:35, 19 April 2017
Contents
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
Feature | Type | Submitted by | Status |
---|---|---|---|
Updating chemistry rate constants based on JPL Publication 15-10 | Science | Barron Henderson (US EPA) Mat Evans (U. York) Oxidants and Chemistry WG |
In progress |
Fixes to correct ALK4 lumping issue | Science | Barron Henderson (US EPA) | " " |
PAN updates | Science | Emily Fischer (CSU) | " " |
Monthly mean NEI2011 emissions | Science | GCST Katie Travis (Harvard) |
" " |
Implement ISORROPIA v2.0 as a Fortran module (eliminating COMMON blocks)
|
Structural | Seb Eastham (Harvard) GCST |
" " |
Updates to the HEMCO emissions component: | Structural & Bug fix |
Christoph Keller (NASA GMAO) Seb Eastham (Harvard) Jessica Morena (Dalhousie) GCST Brian Boys (Dalhousie) |
" " |
Updates to gain computational speedup: | Structural & Bug fix |
Mike Long (Harvard) Bob Yantosca (GCST) |
" " |
Bug fixes in the GEOS-Chem sulfate module: | Bug fix | Prasad Kasibhatla (Duke) Qianjie Chen (UW) Viral Shah (UW) |
" " |
Fix bug in computation of dry deposition aerodynamic resistance Ra | Bug fix | Brian Boys (Dalhousie) | " " |
Fixed typo in nested-grid transport routine INIT_WINDOW | Bug fix | Bob Yantosca (GCST) | " " |
netCDF file I/O updates: | Bug fix & Structural |
Chris Holmes (Florida State) Andy Jacobson (NOAA) GCST |
" " |
Makefile and build sequence updates: | Bug fix & Structural |
Jiawei Zhang (Harvard) GCST |
" " |
Bug fixes for running UCX in ESMF environment | Bug fix | Christoph Keller (NASA GMAO) | " " |
Bug fix in cos(SZA) for start of timestep | Bug fix | Lizzie Lundgren (GCST) | " " |
Bug fixes for diagnostics: | Bug fix | Aaron van Donkelaar (Dalhousie) Jenny Fisher (U. Wollongong) GCST Chris Holmes (Florida State) |
" " |
Removal of obsolete variables: | Structural | GCST | " " |
Include TOA pressure when calculating dry pressure edges for advection and unit conversions | Science | Seb Eastham (Harvard) | " " |
Fix acetone parameterization in hcox_seaflux_mod.F90 | Bug fix | GCST | " " |
v11-02b
Feature | Type | Submitted by | Status |
---|---|---|---|
Merge GCHP source code updates with GEOS-Chem v11-01a | Structural | GCHP development team GCST |
v11-02c
Feature | Type | Submitted by | Status |
---|---|---|---|
Updates to isoprene chemistry, includes:
|
Science | Jenny Fisher (U. Wollongong) Eloïse Marais (Harvard) Kelvin Bates (Caltech) Katie Travis (Harvard) |
|
Enhance default GEOS-Chem simple SOA | Science | Aerosols Working Group |
|
Add aqueous isoprene uptake to SOA scheme | Science | Eloise Marais (Harvard) |
|
Bug fixes for the ND50 timeseries diagnostic | Bug fix | Chris Holmes (Florida State) |
|
Fixed an incorrect format statement in input_mod.F | Bug fix | Chris Holmes (Florida State) |
|
Now use YYYYMMDDhhmm for time stamp values | Bug fix | Andy Jacobson (NOAA) GCST |
|
v11-02d
Feature | Type | Submitted by | Status |
---|---|---|---|
Halogen chemistry updates | Science | Tomás Sherwen (York) Johan Schmidt (Harvard) Oxidants and Chemistry WG |
v11-02e
Feature | Type | Submitted by | Status |
---|---|---|---|
Update density of BC to 1.8 and add absorption enhancement factor in input.geos | Science | Xuan Wang (MIT) |
|
Monthly mean surface methane distributions | Science | Lee Murray (NASA GISS/LDEO) | |
Radon flux diagnostic | Benchmark | GCST | |
UCX stratospheric water boundary condition update | Science | Chris Holmes (UC Irvine) Seb Eastham (Harvard) |
|
In the pipeline
Feature | Type | Submitted by | Status |
---|---|---|---|
Compile with PRECISION=4 as the default–declare most real variables as REAL*4 instead of REAL*8 | Structureal | GCST |
|
EDGAR v4.3 emissions | Science | Chi Li (Dalhousie) |
|
EPA-derived BC/OA emissions over US (1990-2012) | Science | David Ridley (MIT) | |
Historical CAC emissions | Science | Chi Li (Dalhousie) |
|
Ammonia from Arctic birds | Science | Dalhousie group | |
Ocean ammonia emission inventory | Science | Fabien Paulot (NOAA/GFDL) |
|
A snow NOx source from deep snowpack | Science | Maria Zatko (UW) Becky Alexander (UW) |
|
Non-agricultural NH3 for use with MASAGE | Science | Amos Tai (CUHK) | |
Anthropogenic PM2.5 dust source | Science | Sajeev Philip (Dalhousie) |
|
Fix to direct/diffuse radiation | Science | Katie Travis (Harvard) | |
Species Database Phase 3:
|
Science | GCST | |
Updated organic deposition | Science | Katie Travis (Harvard) Jenny Fisher (U. Wollongong) |
|
Remove dependence of species drydep on HNO3 drydep | Science | Katie Travis (Harvard) Jenny Fisher (U. Wollongong) |
|
Update SO2 scavenging in convective updrafts for consistency | Science | Duncan Fairlie (NASA/LARC) | |
Sedimentation of stratospheric aerosols | Science | Sebastian Eastham (Harvard) | |
Uniformity of units | Structural | GCST |
|
NetCDF Output Phase 3a: Output diagnostics in NetCDF format | Structural | GCST | |
NetCDF Output Phase 3b: Updates to eliminate differences between single and multi-segmented GEOS-Chem runs | Bug fix/Structural | GCST Christoph Keller |
|
PCB simulation | Science | Carey Friedman (MIT) Helen Amos (Harvard) |
|
Hg code updates (chemistry, ocean, land) | Science | Hg and POPs Working Group | |
Surface ocean Hg boundary conditions from MITgcm | Science | Hannah Horowitz (Harvard) | |
Additional modifications for FlexChem, including:
|
Structural | Mike Long (Harvard) GCST |
|
FlexGrid: Use HEMCO I/O and regridding capabilities to read and regrid met fields | Structural | Jiawei Zhuang (Harvard) Jintai Lin (PKU) |
|
Merge standard simulation with specialty simulations for OVOC, acids, aromatics, dicarbonyls, terpenes | Science | Dylan Millet (UMN) Xin Chen (UMN) |
|
Nested CO2, CH4, Hg, TOMAS, adjoint, etc. | Science | Nested Model Working Group | |
Update ISORROPIA from v2.0 to v2.2, in order to remove persistent noise in output | Science | Seb Eastham (Harvard) |
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:
(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 beDIVISOR=COUNT
for allND50_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)
Outstanding issues not yet resolved in GEOS-Chem v11-02
TBD