Difference between revisions of "GEOS-Chem 12"

From Geos-chem
Jump to: navigation, search
(Outstanding issues not yet resolved in GEOS-Chem v11-03)
(FlexChem bug fix: do not zero ACTA, EOH, HCOOH)
Line 449: Line 449:
=== FlexChem bug fix: do not zero ACTA, EOH, HCOOH ===
=== FlexChem bug fix: do not zero ACTA, EOH, HCOOH ===
<span style="color:darkorange">'''''This fix will be included in v11-03.'''''</span>
<span style="color:darkorange">'''''This fix will be included in GEOS-Chem 12.'''''</span>
'''''[[User:Katherine Travis|Katie Travis]] wrote:'''''
'''''[[User:Katherine Travis|Katie Travis]] wrote:'''''

Revision as of 15:37, 20 June 2018

GEOS-Chem v11-02-final will also carry the designation GEOS-Chem 12.0.0. We are migrating to a purely numeric versioning system in order to adhere more closely to software development best practices. For a complete description of the new versioning system, please see our GEOS-Chem version numbering system wiki page.

Version history

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

Previous major release This version in development Next major release
GEOS-Chem v11-02 (aka 12.0.0) GEOS-Chem 12 GEOS-Chem 13
View v11-02 benchmark history View GEOS-Chem 12 benchmark history TBD

GEOS-Chem 12.3.0

GEOS-Chem 12.2.0

GEOS-Chem 12.1.0

GEOS-Chem 12.0.0

In order to transition to a new, purely numeric versioning system, the GEOS-Chem v11-02-final release also carries the designation GEOS-Chem v12.0.0

For a complete description of the new versioning system, please see our GEOS-Chem version numbering system wiki page.

--Bob Yantosca (talk) 15:35, 20 June 2018 (UTC)

In the pipeline

The table below lists features that will eventually be added into GEOS-Chem. Please also see our GEOS-Chem model development priorities page.

Feature Submitted by Type Status
Bug fixes (to be implemented ASAP)
FlexChem bug fix: do not zero ACTA, EOH, HCOOH Katie Travis (MIT)
Mike Long
Sebastian Eastham (MIT)
Bug Fix
  • This can go into v11-03 right away.
Avoid double counting CEDS and GEIA NH3 biofuel emissions Eloise Marais (Birmingham) Bug Fix
  • The fix involves a simple change to the HEMCO_Config.rc file. This can go into v11-03 right away.
Fix double counting of CO2 emissions in CO2 simulations Beata Bukosa (UW) Bug fix
  • Awaiting code from developer
Transport updates
GEOS resolution & subgrid convection Karen Yu (Harvard) Science
  • Delivered to GCST (Oct 2017)
Common set of tracers in GEOS-Chem and GEOS Transport WG
Chemistry updates
Heterogeneous uptake of NOx species by cloud droplets Chris Holmes (FSU) Science
Updated chlorine chemistry Xuan Wang (Harvard) Science
Extend UCX into the mesosphere Sebastian Eastham (MIT) Science
Add ND49 timeseries diagnostic for correcting ozone from the height of the lowest model level to 10m Katie Travis (MIT) Structural
  • Waiting on publication of a paper
Emissions updates
OMI-based Volcanic emissions 2005-2012 Cui Ge (U. Iowa)
Jun Wang (U. Iowa)
  • A fix needs to be implemented to skip over missing data files (the data set ends in Sep 2012). Otherwise simulations will die when files are not found.
EPA NEI2011 Version EK Zitely Tzompa-Sosa (CSU)
Emily Fischer (CSU)
  • We need more time to do a proper validation of this inventory.
FINNv1.6 biomass burning emissions for 2014-2016 Barron Henderson (US EPA) Science
Anthropogenic PM2.5 dust source Sajeev Philip (Dalhousie) Science
  • Need to fix an under-the-hood issue in HEMCO that makes this update yield 1200 Tg of dust.
MEIC emissions over China (2000-2015) Lu Shen (Harvard)
Melissa Sulprizio (Harvard)
  • Postponed until the MEIC paper is published.
Grid-independent emissions, including:
  • Lightning NOx emissions (3-hourly)
  • Dust emissions (hourly)
  • Biogenic and sea salt emissions (hourly)
Randall Martin (Dalhousie)
Lee Murray (Rochester)
David Ridley (MIT)
Jintai Lin (PKU)
  • Mostly ready; need to download data from developers
EPA-derived BC/OA emissions over US (1990-2012) David Ridley (MIT)
Chi Li (Dalhousie)
  • Need to coordinate between Ridley and Li versions
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)
  • 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)
Non-agricultural NH3 for use with MASAGE Amos Tai (CUHK) Science
Radon emission update Bo Zhang (NIA/NASA Langley) Science
  • Delivered to GCST (Nov 2017)
  • Implementation pending paper submission
GFAS biomass burning emissions Mat Evans (York) Science
Deposition/surface updates
Wet scavenging in mixed-phase clouds Bo Zhang (NIA/NASA Langley) Science
  • Delivered to GCST (Nov 2017)
  • Only applied/tested for Pb
  • Implementation pending paper submission
Harmonizing Henry's Law coefficients across wet and dry deposition GCST Science
Sedimentation of stratospheric aerosols Sebastian Eastham (Harvard) Science
Aerosol updates
Sea salt aerosol alkalinity Qianjie Chen (UW)
Becky Alexander (UW)
Xuan Wang (Harvard)
  • UW version delivered to GCST (Nov 2017)
VBS SOA option Rokjin Park (SNU) 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
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
Africa nested-grid for GEOS-FP and MERRA-2 Eloise Marais (U. Birmingham) Science
  • Delivered to GCST (Dec 2017)
West Africa nested-grid for GEOS-FP Mat Evans (York)
Eleanor Morris (York)
Tagged sulfate simulation Becky Alexander (UW) Science
Arsenic simulation Shiliang Wu (MT) Science
Structural updates
Updated flux diagnostics Chris Holmes (Florida State)
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)
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
Add total column O3 to benchmarks Chris Holmes (FSU)
Uniformity of units GCST Structural
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
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)
  • 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

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


In this section we provide information about the benchmarks and tests that we have done to validate GEOS-Chem v11-03.

1-month and 1-year benchmarks

For complete information about the benchmark simulations used to validate GEOS-Chem v11-03, please see our GEOS-Chem v11-03 benchmark history wiki page.

Unit tests for GEOS-Chem v11-03

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 v11-03. Click on the links below to see the results from each set of unit tests:

Unit test Date

Previous issues now resolved in GEOS-Chem 12

The following bugs and/or technical issues have been resolved in v11-03.

Outstanding issues not yet resolved in GEOS-Chem 12

The following known issues are slated to be fixed in v11-03:

FlexChem bug fix: do not zero ACTA, EOH, HCOOH

This fix will be included in GEOS-Chem 12.

Katie Travis wrote:

I am working on a VOC simulation, and noticed that in my copy of v11-02f, the following species are set to zero in two places:
     ! Zero certain species
     C(ind_ACTA) = 0.e0_dp
     C(ind_EOH) = 0.e0_dp
     C(ind_HCOOH) = 0.e0_dp
  C(ind_ACTA)  = 0.0_dp
  C(ind_HCOOH) = 0.0_dp
Since none of these species are fixed in Tropchem.eqn, shouldn’t they NOT be set to zero?

Mike Long wrote:'

I think the code should be removed. This must have been a patch added to maintain parity with SMVGEAR w/o anticipating that the species would become active.

--Bob Yantosca (talk) 16:19, 17 May 2018 (UTC)

Avoid double counting CEDS and GEIA NH3 biofuel emissions

This fix will be included in v11-03.

Eloise Marais wrote:

If CEDS includes NH3 emissions, then this will be double counting. I recommend using CEDS, as GEIA is very out of date (1998 according to the HEMCO configuration file I have).

Daniel Jacob replied:

We should use the GEIA NH3 natural emission inventory (1° x 1° file from Eleanor Morris) but not the GEIA NH3 biofuel inventory.

--Bob Yantosca (talk) 16:33, 17 May 2018 (UTC)