GEOS-Chem v10-01

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Contents

Overview

History

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

Previous version This version Next version
GEOS-Chem v9-02 GEOS-Chem v10-01 GEOS-Chem v11-01
PUBLIC RELEASE 03 Mar 2014 PUBLIC RELEASE 17 Jun 2015 PUBLIC RELEASE 01 Feb 2017
View v9-02 benchmark history View v10-01 benchmark history View v11-01 benchmark history
View v9-02 performance results View v10-01 performance results View v11-01 performance results

--Bob Yantosca (talk) 19:36, 21 December 2016 (UTC)

Period of public comment

The PROVISIONAL RELEASE of GEOS-Chem occurred on 01 May 2015. We ask the GEOS-Chem User Community to download:

  1. the GEOS-Chem v10-01 source code
  2. the corresponding run directories
  3. the corresponding data directories

and to compile and one or more GEOS-Chem simulations.

A period of public comment lasted until 15 Jun 2015. During this time, we asked the GEOS-Chem User Community to report any

  1. Last-minute bugs
  2. Technical issues with the GEOS-Chem code or data
  3. Typos or omissions in the wiki or web documentation
  4. Other issues (i.e. problems downloading or installing the code and/or required libraries)

to the GEOS-Chem Support Team (email geos-chem-support[at]harvard.edu) so that fixes could be implemented. The GEOS-Chem user community identified a number of issues (see this table below). The GEOS-Chem Support Team worked with the GEOS-Chem user community to resolve these issues.

--Bob Y. (talk) 18:45, 16 June 2015 (UTC)

What's new in this version

NOTE: v10-01a, v10-02b, etc. denote 1-month benchmark simulations, which are designed to evaluate GEOS-Chem's performance at intermediate stages of development.

v10-01a

Please see the approval form for 1-month benchmark simulation v10-01a for complete information about the validation of GEOS-Chem v10-01a.

Feature Type Submitted by Status
Updates to dry deposition when using the Olson 2001 land map Science Patrick Kim (Harvard) Approved 05 Feb 2014

--Bob Y. 11:08, 26 February 2015 (EST)

v10-01b

Please see the approval form for 1-month benchmark simulation v10-01b for complete information about the validation of GEOS-Chem v10-01b.

Feature Type Submitted by Status
Now use correct molecular weight for the PROPNN tracer in input.geos Bug fix Jenny Fisher (U. Wollongong) Approved 06 Mar 2014
Use MAP_A2A to regrid 1x1 TOMS O3 to model resolution Structural Jintai Lin (Peking U.) " "

--Bob Y. 11:08, 26 February 2015 (EST)

v10-01c

Please see the following links for complete information about the validation of GEOS-Chem v10-01c:

  1. Approval form for 1-month benchmark simulation v10-01c
  2. Results for 1-year benchmark simulation v10-01c-Run0
  3. Results for 1-year benchmark simulation v10-01c-Run1
Feature Type Submitted by Status
UCX strat chem mechanism, includes: Science UCX:
Sebastian Eastham (MIT)

Fast-JX:
Sebastian Eastham (MIT),
Jingqiu Mao (Princeton)

1-month benchmark:
Approved 29 May 2014

1-year benchmark:
Approved 26 Jun 2014
Bug fix for determining when to use TOMS O3 columns Bug fix GEOS-Chem Support Team " "
Add support for TAU performance profiler Structural John Linford (ParaTools, Inc.)
GEOS-Chem Support Team
" "
Fixes for timeseries diagnostics to allow for more transported tracers Bug fix GEOS-Chem Support Team " "
Fixes for the stratospheric chemistry module Structural GEOS-Chem Support Team " "
Various updates for GEOS-Chem specialty simulations Bug fix &
Structural
Jeff Pierce (CSU)
Kevin Wecht (Harvard)
Matthew Johnson (NASA)
GEOS-Chem Support Team
" "
Updates to speed up GEOS-Chem execution Structural GEOS-Chem Support Team " "

--Bob Y. 11:08, 26 February 2015 (EST)

v10-01d

Please see the approval form for 1-month benchmark simulation v10-01d for complete information about the validation of GEOS-Chem v10-01d.

Feature Type Submitted by Status
Fix error in ISOPO2 isomerization reaction in globchem.dat Bug fix Ploy Achakulwisut (Harvard) Approved 03 Jun 2014
Modify NcdfUtil code to allow re-opening of netCDF "define mode" Structural GEOS-Chem Support Team " "
Fix parallelization error in nested grid simulations Bug fix Jintai Lin (Peking U.) " "
Fixed bug in ND44 drydep diagnostic for sea salt aerosols Bug fix Kateryna Lapina (CU Boulder) " "
Implement final recommendation for J(HAC) and J(PAN) in FAST-JX v7.0 Science Sebastian Eastham (MIT), Jingqiu Mao (Princeton) " "

--Bob Y. 11:08, 26 February 2015 (EST)

v10-01e

Please see the the following links for complete information about the validation of GEOS-Chem v10-01e:

Feature Type Submitted by Status
HEMCO emissions component Structural Christoph Keller (Harvard)
GEOS-Chem Support Team
GMAO
1-month benchmark:
Approved 07 Nov 2014

1-year benchmark:
Approved 01 Dec 2014
Removing references to modules made obsolete by GIGC and HEMCO Structural GEOS-Chem Support Team " "
Reactivating dust tracers in TOMAS simulations Bug fix Jeff Pierce (CSU)
David Ridley (MIT)
" "
Fix for ND61 diagnostic in TOMAS simulations Bug fix Betty Croft (Dalhousie) " "

--Bob Y. 11:08, 26 February 2015 (EST)

v10-01f

Please see the approval form for 1-month benchmark simulation v10-01f for complete information about the validation of GEOS-Chem v10-01f.

Feature Type Submitted by Status
Two-way coupling between global and nested GEOS-Chem models Science Jintai Lin (Peking U.)
Yingying Yan (Peking U.)
Approved 13 Jan 2015
Update ALD2 photolysis in FAST-JX v7.0 Science Jingqiu Mao (Princeton), Sebastian Eastham (MIT) " "
Read 2D data for individual NOx species in ucx_mod.F Bug fix Sebastian Eastham (MIT) " "
Bug fixes and updates for tagged CO simulation Bug fix Jenny Fisher (U. Wollongong) " "
Bug fixes for scavenging by co-condensation Bug fix Duncan Fairlie (NASA LaRC) " "
Correct bugs in stratospheric Bry data Bug fix Johan Schmidt (Harvard) " "
Introduction of flexible precision into GEOS-Chem Structural GEOS-Chem Support Team " "
Updates for 0.25° x 0.3125° China nested grid with GEOS-FP meteorology Structural Yuxuan Wang (Tsinghua/Galveston) " "
Additional minor updates to HEMCO Structural Christoph Keller (Harvard) " "

--Bob Y. 11:08, 26 February 2015 (EST)

v10-01g

This version included all bug fixes, so we did not run a benchmark for v10-01g. Instead, the fixes added in this version were validated with the v10-01h benchmarks.

Feature Type Submitted by Status
Add fix to prevent a segmentation fault in HEMCO when emissions are turned off Bug fix Christoph Keller (Harvard) Approved 01 May 2015
Bug fix in planeflight diagnostic when using short chemistry timesteps Bug fix Luke Schiferl (MIT) " "
Fix calculation of WETLOSS for non-aerosol tracers in DO_MERRA_CONVECTION and DO_WASHOUT_ONLY Bug fix Carey Friedman (MIT) " "
Make the netCDF library linking process more portable Structural Bob Yantosca (Harvard) " "

--Bob Y. 11:08, 26 February 2015 (EST)

v10-01h

Please see the the following links for complete information about the validation of GEOS-Chem v10-01h:

Feature Type Submitted by Status
FINNv1 biomass burning emissions (optional inventory implemented via HEMCO) Science Jenny Fisher (U. Wollongong)
Jingqiu Mao (Princeton)
Christine Wiedinmyer (NCAR)
  • Jun Wang (U. Nebraska) and colleagues are updating FINN emissions to present date
Approved 01 May 2015
  • NOTE: It was discovered that ship emissions had been turned off inadavertently due to a bug in HEMCO in this benchmark. The fix was corrected in v10-01i and validated with both 1-month and 1-year benchmarks.
GFED4 biomass burning emissions (implemented via HEMCO) Science Prasad Kasibhatla (Duke)
Christoph Keller (Harvard)
" "
Add Guenther et al (2012) updates to MEGAN2.1 biogenic emissions (implemented via HEMCO) Science Dylan Millet (U. Minnesota) " "
Updates to ship NOx chemistry, includes: Science & Bug fix Chris Holmes (UC Irvine)
Geert Vinken (Eindhoven)
" "
MASAGE NH3 agricultural emissions (optional inventory implemented via HEMCO) Science Fabien Paulot (Harvard) " "
Replace EDGARv3 with EDGAR v4.2 anthropogenic emissions (implemented via HEMCO) Science Qiang Zhang (Tsinghua)
Meng Li (Tsinghua)
Sajeev Philip (Dalhousie)
" "
HTAP emissions (optional inventory implemented via HEMCO) Science Qiang Zhang (Tsinghua) " "
MIX Asian emissions (implemented via HEMCO) Science Qiang Zhang (Tsinghua)
Meng Li (Tsinghua)
" "
NEI 2011 emissions with hourly resolution (implemented via HEMCO) Science Katie Travis (Harvard) " "
Update EMEP emissions for 2008-2010 (implemented via HEMCO) Science Aaron van Donkelaar (Dalhousie) " "
Update OTD/LIS factors for GEOS-FP through October 2014 (implemented via HEMCO) Science Lee Murray (Columbia) " "
Re-implement RCP future emission scenarios via HEMCO Structural Christoph Keller (Harvard)
Chris Holmes (Florida State)
" "
Split AEROCOM volcanic emissions back into eruptive and degassing (implemented via HEMCO) Structural Christoph Keller (Harvard) " "
Additional updates to HEMCO Structural Christoph Keller (Harvard) " "
Fix for optimization error discovered in v10-01h Bug fix GEOS-Chem Support Team " "

--Bob Y. 15:13, 4 May 2015 (EDT)

v10-01i

Please see the the following links for complete information about the validation of GEOS-Chem v10-01i:

  1. Approval form for 1-month benchmark simulation v10-01i with RRTMG off
  2. Approval form for 1-month benchmark simulation v10-01i with RRTMG on
  3. Results for 1-year benchmark simulation v10-01i-Run0
Feature Type Submitted by Status
Online Radiative Transfer in GEOS-Chem Science David Ridley (MIT),
Colette Heald (MIT)
  • 1-month benchmark:
    Approved 30 Apr 2015
  • 1-year benchmark:
    Approved 01 May 2015
Reprocessed EMEP emissions for 1990-2012 Science Aaron van Donkelaar (Dalhousie) " "
Bug fixes for the PARANOX HEMCO extension Bug fix Christoph Keller (Harvard) " "
Reprocessed AEIC emissions Bug fix Christoph Keller (Harvard) " "
CO2 simulation emission updates, includes:
  • Simple Biosphere (SiB3) model balanced biosphere fluxes (2006-2010)
  • Scaled Takahashi et al. (2009) Ocean CO2 fluxes for 2000-2013
  • ODIAC v2013 national fossil fuel combustion emissions for 2000-2014
  • TIMES weekly and diurnal fossil fuel temporal scaling factors
  • Extended time range for CDIAC, chemical CO2 source, shipping and aviation scale factors
Science Ray Nassar (Environment Canada) " "
Now call the planeflight diagnostic after chemistry Bug fix Karen Yu (Harvard) " "
Updates for the 0.25° x 0.3125° nested-grid simulations Structural Lin Zhang (PKU) " "
Remove obsolete drydep species ISN2 Structural Katherine Travis (Harvard) " "
Add new features to HEMCO for v10-01i Structural Christoph Keller (Harvard) " "

--Bob Y. 16:03, 1 May 2015 (EDT)

Last-minute fixes for the GEOS-Chem v10-01 provisional release

The following updates were added as last-minute fixes before the provisional-release of GEOS-Chem v10-01. These submissions fix issues that were brought to our attention after the v10-01i benchmarks were submitted.

Feature Type Submitted by Status
Avoid errors when MEGAN biogenic emissions are used with monoterpenes turned off (i.e. MEGAN_mono = false) Bug fix Christoph Keller (Harvard) Released on 01 May 2015
Restore missing diagnostic: "Biogenic CO from monoterpenes" Bug fix GEOS-Chem Support Team " "
Remove Russia from MIX Asia mask file Bug fix Qiang Zhang (Tsinghua)
Meng Li (Tsinghua)
" "

--Melissa Sulprizio 15:38, 11 May 2015 (EDT)

Fixes and updates added during the public comment period

The following updates were added during the Period of Public Comment for GEOS-Chem v10-01, which lasted from 01 May 2015 to 15 Jun 2015.

Please see the following links for complete information about the validation of GEOS-Chem v10-01-public-release:

Feature Type Submitted by Status
Switching to the officially released GFED4 data files Science Prasad Kasibhatla (Duke), Christoph Keller (Harvard) 1-month benchmarks:
Approved 16 Jun 2014

Rn-Pb-Be benchmark:
Approved 16 Jun 2014
Fixing some last-minute technical issues with RRTMG Science David Ridley (MIT)
GEOS-Chem Support Team
" "
Now use the correct version of FAST-JX input file org.dat Bug fix David Ridley (MIT) " "
Adding QFED2 biomass burning as an option Science Katie Travis (Harvard), Christoph Keller (Harvard) " "
Add more years of latitudinal CH4 data Science Katie Travis (Harvard)
Lee Murray (NASA GISS/LDEO)
" "
Minor bug fix in gamap_mod.F Bug fix Sebastian Eastham (MIT) " "
Bug fixes for the PGI compiler Bug fix Gan Luo (SUNY/Albany)
GEOS-Chem Support Team
" "
Modifications to Makefile_header.mk Structural GEOS-Chem Support Team " "
Fixed typo for BROMOCARB_SEASON in HEMCO configuration files Bug fix Luke Schiferl (MIT)
GEOS-Chem Support Team
" "
Updates to HEMCO made during v10-01 period of public comment Structural Christoph Keller (Harvard) " "
Bug fix in I3 field interpolation Bug fix GEOS-Chem Support Team " "
Updated name of ICOADS_SHIP files in HEMCO configuration files Bug fix GEOS-Chem Support Team " "
Avoid PARANOX SUNCOS error by using the proper timestamps Bug fix GEOS-Chem Support Team " "
Bug fixes for the 0.25° x 0.3125° nested EU simulation using GEOS-FP meteorology Bug fix Anna Protonatariou (Athens) " "
Additional fixes for MERRA wet deposition Bug fix Viral Shah (UW) " "
Removing additional code made obsolete by HEMCO Structural GEOS-Chem Support Team " "
Add SOA tracers to the GEOS-Chem benchmark simulation Structural GEOS-Chem Support Team " "
Fix AEFs for sesquiterpenes in the SOA simulation Bug fix GEOS-Chem Support Team " "
Other miscellaneous updates Bug fix GEOS-Chem Support Team " "
Continuing into v11-01
Finalizing flexible precision updates Structural GEOS-Chem Support Team
  • Code updates are mostly in place.
  • Benchmarking and further testing/debugging will continue into v11-01.
Adding documentation to describe internal changes made to GMAO met field products Structural NASA/GMAO
GEOS-Chem Support Team
Resolve issues in the ocean mercury simulation Bug fix Hg and POPs Working Group
GEOS-Chem Support Team
  • This effort will continue into v11-01.
Make TOMAS compatible with HEMCO Structural Jack Kodros (CSU)
Jeff Pierce (CSU)
GEOS-Chem Support Team
  • The latest updates were added into v10-01.
  • The TOMAS team is doing further validation, which will continue into v11-01

--Bob Y. (talk) 18:16, 16 June 2015 (UTC)
--Bob Yantosca (talk) 18:59, 2 February 2016 (UTC)

New data directories

The following new data directories have been added for GEOS-Chem v10-01. You will have to download the directories relevant to your simulation.

All data directories are now subdirectories of ExtData

The data directory tree used by GEOS-Chem v10-01 has been modified such that all data directories are now subdirectories of a single root folder named ExtData. For more information, please see our Setting up the ExtData directory wiki page.

--Bob Y. 17:54, 28 April 2015 (EDT)

Files for the UCX chemistry mechanism

The UCX chemistry mechanism requires data located in this directory:

$ROOTDIR/ExtData/CHEM_INPUTS/UCX_201403                    # Input files for the UCX mechanism

where $ROOTDIR is the top-level data directory on your system. (If you don't know where that is, ask your sysadmin.)

You can download these directories with anonymous FTP or the Wget utility. For instructions, please visit the following pages:

--Bob Y. 17:56, 28 April 2015 (EDT)

Emissions files for use with HEMCO

In GEOS-Chem v10-01 and newer versions, emissions are computed by the HEMCO emissions component and are passed to GEOS-Chem. We have created new data files (in COARDS-compliant netCDF format) for use with HEMCO. These new data files are contained in the HEMCO data directory tree. For detailed instructions on how to download these data files to your disk server, please see our Downloading the HEMCO data directories wiki post.

We recommend placing the HEMCO data in the directory path

$ROOTDIR/ExtData/HEMCO                             

where $ROOTDIR is the top-level data directory on your system. (If you don't know where that is, ask your sysadmin.)

Also see our The Setting up the ExtData directory wiki page for more information about the top-level ExtData directory.

--Bob Y. 17:34, 28 April 2015 (EDT)

Validation

In this section we provide information about the benchmarks and tests that we have done to validate GEOS-Chem v10-01.

1-month and 1-year benchmarks

For complete information about the benchmark simulations used to validate GEOS-Chem v10-01, please see our GEOS-Chem v10-01 benchmark history wiki page.

--Bob Y. 16:09, 30 April 2015 (EDT)

Unit tests for GEOS-Chem v10-01

We performed a full set of unit tests on GEOS-Chem before submitting each 1-month benchmark. Click on the links below to see the results from each set of unit tests:

Unit test Date Notes
v10-01c 29 May 2014
v10-01d 03 Jun 2014
  • Unit tests for tagged CO and TOMAS were not performed, since these simulations are not yet 100% compatible with HEMCO.
v10-01e 07 Nov 2014
  • Unit tests for tagged CO and TOMAS were not performed, since these simulations are not yet 100% compatible with HEMCO.
v10-01f 13 Jan 2015)
  • Unit tests for tagged CO and TOMAS were not performed, since these simulations are not yet 100% compatible with HEMCO.
v10-01g 26 Feb 2015
  • Unit tests for tagged CO and TOMAS were not performed, since these simulations are not yet 100% compatible with HEMCO.
v10-01h 27 Mar 2015
  • Unit tests for tagged CO and TOMAS were not performed, since these simulations are not yet 100% compatible with HEMCO.
  • Numerical noise differences were apparent in the ocean Hg restart file for the geos5_2x25_Hg simulation. We were unsure why this occurred, and think it was due to an issue in HEMCO that was later resolved.</code>.
v10-01i 20 Apr 2015
  • Unit tests for tagged CO and TOMAS were not performed, since these simulations are not yet 100% compatible with HEMCO.
  • Due to a change in queue time limits, we were not able to submit unit tests at 2° x 2.5° or finer resolution.
v10-01-provisional 28 May 2015
  • Unit tests for tagged CO were not performed, since this simulations are not yet 100% compatible with HEMCO.
  • The TOMAS unit tests have been restored
  • We also did unit tests for 2° x 2.5° and nested grid "tropchem" and "UCX" simulations.
v10-01-public-release 16 Jun 2015
  • Unit tests for tagged CO were not performed, since this simulations are not yet 100% compatible with HEMCO.

--Bob Y. (talk) 14:51, 16 June 2015 (UTC)

Previous issues now resolved in GEOS-Chem v10-01

The following bugs and/or technical issues have now been resolved in GEOS-Chem v10-01.

Now use correct value of molecular weight for the PROPNN tracer in input.geos

This update was validated in the 1-month benchmark simulation v10-01b and approved on 06 Mar 2014.

This unresolved issue from GEOS-Chem v9-02 has now been corrected.

--Bob Y. 15:45, 12 March 2014 (EDT)

Now use MAP_A2A to regrid 1x1 TOMS O3 to model resolution

This update was validated in the 1-month benchmark simulation v10-01b and approved on 06 Mar 2014.

For complete information about this issue, please see this post on our FAST-J photolysis mechanism wiki page.

--Bob Y. 15:47, 12 March 2014 (EDT)

Bug fix for determining when to use TOMS O3 columns

This update was validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.

For complete information about this issue, please see this post on our FAST-J photolysis mechanism wiki page.

--Bob Y. 16:58, 30 May 2014 (EDT)

Fixes for the stratospheric chemistry module

These updates were validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.

We have introduced the following fixes to the stratospheric chemistry module. Please see the following posts for more information:

  1. Reduce memory footprint of the stratospheric chemistry module
  2. Bug fix in routine GET_RATES_INTERP. affecting nested-grid simulations

--Bob Y. 16:58, 30 May 2014 (EDT)

Various updates for GEOS-Chem specialty simulations

These updates were validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.

We have added several updates (both structural updates and minor bug fixes) to the GEOS-Chem specialty simulations. Please view the following posts for more information:

Simulation Status Updates
C2H6 simulation Needs attention
  • The C2H6 simulation is initialized with a call from routine GIGC_Init_Extra in module GeosCore/input_mod.F.
CH4 simulation Up-to-date
HCN/CH3CN simulation Needs attention
  • The HCN/CH3CN simulation is initialized with a call from routine GIGC_Init_Extra in module GeosCore/input_mod.F.
Tagged CO simulation Up-to-date
Hg + Global Terrestrial Mercury Model Up-to-date
POPs simulation Up-to-date
Tagged O3 simulation Up-to-date
TOMAS aerosol microphysics Up-to-date

NOTE: Initializing the various specialty simulations from routine GIGC_Init_Extra is necessaary for compatibility with our Grid-Independent GEOS-Chem (aka GIGC) development. We need to initialize all GEOS-Chem simulations at the start of the simulation, and not on the first chemistry or emissiosn timestep after the simulation has already started. This is a requirement of the Earth System Model Framework (ESMF) software upon which our GIGC code relies.

--Bob Y. 16:58, 30 May 2014 (EDT)

Updates to speed up GEOS-Chem execution

These updates were validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.

We used the GEOS-Chem Unit Tester and the Tuning and Analysis Utilities (TAU) to locate and fix the following inefficiencies in GEOS-Chem:

Location Problem Solution
Olson land map module Performance bottleneck Speed up computations in subroutine COMPUTE_OLSON_LANDMAP
GEOS-4 convection module Array temporary Removed array temporaries in the call to the GEOS-4 convection routine
GCAP convection module Array temporary Removed array temporaries in the call to the GCAP convection routine
Ocean mercury module Array temporary Removed array temporaries in subroutine READ_HG2_PARTITIONING
GEOS-5 / GEOS-FP / MERRA advection module Passing a pointer to an explicit-shape array (inefficiency) Reduce time spent in advection driver routine TPCORE_FVDAS
GEOS-FP / MERRA convection module Inefficient load balancing Reduce time spent in routine DO_CONVECTION when using GEOS-FP or MERRA

--Bob Y. 16:59, 30 May 2014 (EDT)

Bug fixes and and updates for v10-01d

These updates were validated in the 1-month benchmark simulation v10-01d and approved on 03 Jun 2014.

GEOS-Chem v10-01d contains fixes for the following minor issues:

Location Problem Solution
globchem.dat input file Typo in RIO2 reaction Remove duplicate GLYX product from RIO2 reaction
NcdfUtil/m_netcdf_io_define.F90 Need to re-open netCDF define mode to facilitate HEMCO I/O Added routine NcBegin_Def to open or re-open the netCDF define mode. Turning on define mode lets you to define a netCDF variable and all its attributes. But before you can write the actual data to the netCDF file, you first have to switch to data mode. Being able to switch between define mode and data mode frees you from the restriction of having to define all netCDF variables and attributes in a single step.
GeosCore/tpcore_geos5_window_mod.F90
GeosCore/tpcore_geosfp_window_mod.F90
Parallelization bug in nested grid simulations Fix parallelization error in nested grid simulations
GeosCore/seasalt_mod.F The ND44 dry dep diagnostic was not being archived properly when the non-local PBL mixing option was turned off (i.e. when using TURBDAY full PBL mixing). Fixed bug in ND44 drydep diagnostic for sea salt aerosols
Full-chemistry input files:
  • globchem.dat
  • FJX_spec.dat
Implement the final recommendation for J(HAC) and J(PAN). We were not able to include this in the 1-month benchmarks for v10-01c. But these were included in the 1-year benchmarks for v10-01c. Final recommendation for J(HAC) and J(PAN)

--Bob Y. 17:20, 3 June 2014 (EDT)

Reactivating dust tracers in TOMAS simulations

These updates were validated with the 1-month benchmark simulation v10-01e and approved on Approved 07 Nov 2014.

The TOMAS team has submitted a fix that allows you to use the online dust tracers in TOMAS simulations. Due to a bug in input_mod.F, this capability had been omitted. For more information, please see this post on our TOMAS aerosol microphysics wiki page.

--Bob Y. 16:15, 13 June 2014 (EDT)

Fix for ND61 diagnostic in TOMAS simulations

These updates were validated with the 1-month benchmark simulation v10-01e and approved on Approved 07 Nov 2014.

Betty Croft submitted a fix for the ND61 diagnostic (TOMAS nucleation rates). For more information, please see this post on our TOMAS aerosol microphysics wiki page.

--Melissa Sulprizio 10:28, 17 September 2014 (EDT)

Bug fixes and and updates for v10-01f

These updates were validated with the 1-month benchmark simulation v10-01f and approved on Approved 13 Jan 2015.<?span>

GEOS-Chem v10-01f contains fixes for the following minor issues:

Location Problem Solution
Input file FJX_spec.dat Jingqiu Mao (Princeton) and Chris Chan Miller (Harvard) had discovered that the acetaldehyde photolysis rate in FAST-JX v7.0 was incorrect. This has now been corrected in GEOS-Chem v10-01f. For a complete description of the issue, please see this post on our FAST-JX v7.0 photolysis mechanism wiki page.
GeosCore/tagged_co_mod.F Several minor issues were corrected in the Tagged CO simulation. For more information, please see this post on our Tagged CO simulation wiki page.
GeosCore/ucx_mod.F Added 2-D boundary conditions for each of the individual NOx family species. For more information, please see this post on our UCX chemistry mechanism wiki page.
GeosCore/wetscav_mod>F Corrected incorrect values of constants used for the scavenging of H2O2 and NH3 by co-condensation. For more information, please see this post on our Wet deposition wiki page.
GeosCore/strat_chem_mod.F90
and HEMCO routines
Now use updated files for stratospheric Bry concentrations. Data are now placed on the 2° x 2.5° grid and regridded to other resolutions via the HEMCO emissions component. For more information, please see this post on our Bromine chemistry mechanism wiki page.
Various Corrected technical issues in the 0.25° x 0.3125° CH nested grid simulation. For more information, please see this post on our Nested Model Working Group wiki page.
Various Added new functionality into HEMCO. For more information, please see this post on our Implementation of HEMCO in GEOS-Chem wiki page.

--Bob Y. 18:10, 13 January 2015 (EST)

Bug fixes and and updates for v10-01g

GEOS-Chem v10-01g contains fixes for the following minor issues:

Location Problem Solution
GeosCore/hcoi_gc_main_mod.F90
and various other modules
Turning off emissions in the input.geos file made some HEMCO pointers undefined. When other parts of GEOS-Chem tried to access these pointers, a segmentation fault would occur, which would halt GEOS-Chem execution. For a complete description of the solution, please see this post on our Implementation of HEMCO in GEOS_Chem wiki page.
GeosCore/planeflight_mod.F When running a nested simulation with short timesteps, the TAU values (hours since 01 Jan 1985) that are used to define the beginning and end of a chemistry timestep lack the necessary precision. This can cause desired flight points on the edge of chemistry timesteps to not be written out to the planeflight log file. Now use the year, month, day, hour, and minute values obtained from time_mod.F to gain extra precision when computing this particular TAU value.
GeosCore/convection_mod.F
GeosCore/wetscav_mod.F
There is a bug in the calculation of WETLOSS in DO_MERRA_CONVECTION and DO_WASHOUT_ONLY that causes mass of scavenged tracer passed to depo_mercury_mod.F to differ from the mass that is archived in the wet deposition diagnostics (ND38 and ND39). For a complete description of the solution, please see this post on our Wet deposition wiki page.
Makefile_header.mk Some users who have built the netCDF and/or HDF5 libraries with the GEOS-Chem-Libraries installer have reported that GEOS-Chem compiliation dies because the netCDF and/or HDF5 libraries could not be found. This almost always happens if the libraries were built in one directory but later moved to a different directory. For a complete description of this solution, please this post on our Installing libraries for GEOS-Chem wiki page.

--Bob Y. 16:40, 13 January 2015 (EST)

Bug fixes and updates for v10-01h

GEOS-Chem v10-01h contains fixes for the following minor issues:

Location Problem Solution
GeosUtil/grid_mod.F90 An apparent optimization error was overwriting the YSIN array to -1's and 0's, which should not have happened. The HEMCO emissions component relied on the YSIN array to regrid emission fields. As a result of this error, simulations were dying with a segmentation fault. For a complete description of the solution, please see this post on our Regridding in GEOS-Chem wiki page.

--Bob Y. 17:12, 1 April 2015 (EDT)

Bug fixes and updates for v10-01i

GEOS-Chem v10-01i contains fixes for the following minor issues:

Location Problem Solution
GeosCore/drydep_mod.F
GeosCore/tracerid_mod.F
The dry deposition module still referred to obsolete drydep species ISN2. This has now been replaced by ISN1. For a complete description of the solution, please see this post on our Dry deposition wiki page.
GeosCore/main.F Karen Yu noted that the plane flight diagnostic was being written out right after emissions, rather than after chemistry, which was biasing the results, particularly for things like NOx and isoprene. The PLANEFLIGHT routine (in GeosCore/planeflight_mod.F is now called after chemistry.
GeosUtil/regrid_a2a_mod.F90 Regional emissions data files (e.g. EMEP, MIX, NEI2011) as read in by HEMCO were being regridded incorrectly. Negatives were appearing in the arrays for these emissions within the HEMCO data structure. For a complete description of the solution, please see this post on our Regridding in GEOS-Chem wiki page.
Headers/gigc_input_mod.F90
GeosCore/chemistry_mod.F
GeosCore/convection_mod.F
GeosCore/diag_mod.F
GeosCore/pjc_pfix_geosfp_window_mod.F
GeosCore/tpcore_geosfp_window_mod.F90
GeosCore/transport_mod.F
GeosCore/wetscav_mod.F
GeosUtil/bpch2_mod.F
GeosUtil/grid_mod.F90
HEMCO/Extensions/hcox_lightnox_mod.F90
The following issues were observed in the 0.25° x 0.3125° nested-grid simulations:
  • Incorrect latitude edge values were being used
  • Simulations were taking a very long time to run
Lin Zhang (PKU) submitted these fixes for the 0.25° x 0.3125° nested-grid simulations.
  • Now use correct latitude edges.
  • Do not average values over the poles for the nested simulations.
  • Do not run transport over the buffering zone.
  • Implement an option to run the nested simulation over smaller domain to save on time (by changing the buffering zone).
  • Correct a typo in HEMCO/Extensions/hcox_lightnox_mod.F90.

--Bob Y. 11:24, 16 April 2015 (EDT)

Last-minute fixes prior to the GEOS-Chem v10-01 provisional release

Location Problem Solution
Input file HEMCO_Config.rc
HEMCO/Extensions/hcox_megan_mod.F
Turning off monoterpenes in MEGAN (i.e. setting MEGAN_mono to "false" in the configuration file) resulted in array out-of-bounds errors. For a complete description of the solution, please see this post on our Implementation of HEMCO in GEOS-Chem wiki page.
HEMCO/Extensions/hcox_megan_mod.F Biogenic CO emissions from monoterpenes were not being archived. This diagnostic showed zeroes everywhere. A missing subroutine call was restored. For a complete description of the solution, please see this post on our MEGAN v2.1 plus Guenther 2012 biogenic emissions wiki page.
Input file MIX_Asia_mask.generic.025x025.nc The 1-month benchmark simulation for v10-01h showed changes in emissions over Russia caused by the MIX Asia inventory. Qiang Zhang recommends using EDGAR for Russian emissions to obtain consistent emission estimates for Russia. We will use an updated version of MIX_Asia_mask.generic.025x025.nc that does not include Russia. We will retain the old mask file and rename it as MIX_Asia_mask.generic.025x025.w_Russia.nc.

--Melissa Sulprizio 12:51, 6 May 2015 (EDT)

Issues resolved during the public comment period

The following issues were resolved during the Period of Public Comment for GEOS-Chem v10-01, which lasted from 01 May 2015 to 15 Jun 2015.

These updates were validated with the 1-month benchmark simulation v10-01-public-release-Run0 and approved on Approved 16 June 2015.

Switching to the officially released GFED4 data files

Prasad Kasibhatla wrote:

Just a quick note.. The [GFED4] emissions in the [GEOS-Chem v10-01-Provisional release] are a preliminary version. The official first version of GFED4 will be released Mon or Tue (May 4 or 5, 2015). At that point it will simply be a matter of replacing the preliminary data files with the latest files.

--Bob Y. 16:22, 1 May 2015 (EDT)

Bob Yantosca replied:

The GEOS-Chem v10-01 public release will now use the officially-released GFED4 data. These data files are now stored in the HEMCO data directory HEMCO/GFED/v2015-06/ folder, and our hemco_data_download package has been updated accordingly. Please see our HEMCO data directories wiki page for more information.

--Bob Y. (talk) 18:35, 5 June 2015 (UTC)

Technical issues with RRTMG

Dave Ridley wrote:

I think everything is good to go – there is definitely an issue in that the photolysis code isn’t seeing the right aerosol, and this affects things like HNO3 and H2O2 in dust laden regions. But the changes aren’t too dramatic other than those species, so I think we can sign off on the version release and get that sorted during the provisional period.

Bob Yantosca wrote:

There still were a couple more issues (in the v10-01-Provisional release code) that we encountered that need fixing. These are:
  1. Parallelization error in rrtmg_rad_transfer_mod.F. I had to turn off all parallel loops in this module to get the code to pass the unit test. Otherwise you get different results in the ND72 (RADMAP-$) output when you run with parallelization on vs. parallelization off. My turning off the parallel loops will make the code slower but shouldn’t affect the results.
  2. Array temporaries in rrtmg_rad_transfer_mod.F. Some of the calls to RRTMG routines have array temporaries (which can happen if you pass a non-contiguous array slice like ARRAY(:,J,:) to a routine. We can fix these later by using pointers to do the array sub-slicing, and then passing the pointers to the subroutines. Again, this won’t affect the output but will make the code run slower.

Dave Ridley followed up:

I think I may have found the main bug in SET_PROF:
        DO N = 1, NAER
           AERCOL(3+N+NDUST,I) = AEROD(I,N)
        ENDDO

Should be:
        DO N = 1, NAER*NRH
           AERCOL(3+N+NDUST,I) = AEROD(I,N)
        ENDDO

I think the AERCOL is still in the format with an RH bin for each aerosol type, i.e. (NAER*NRH+3+NDUST,LLPAR). When I make that change my idealized tests the J-Values look a lot more like v10.1b.
I also found another glitch in my UCX-RRTMG fix that might have caused an error with the dust too. I need to test the results with the real aerosol (rather than my idealized cases) and also with UCX on to check that the strat aerosols work, but it looks like this will explain the difference.

NOTE: The UCX-RRTMG fix requires a new Fast-JX input file h2so4.dat when using the UCX chemistry mechanism. This file now ships with the GEOS-Chem Unit Tester run directories.

--Melissa Sulprizio (talk) 19:17, 1 June 2015 (UTC)

Bob Yantosca followed up:

The parallelization issue in GeosCore/rrtmg_rad_transfer_mod.F is now fixed. It turned out that in the second parallel loop in this module, we needed to add the variables T_CLIM, Z_CLIM, O3_CLIM, and AIR_CLIM to the !OMP+PRIVATE clause. Having done this, we obtained identical results w/r/t a RRTMG simulation with OpenMP parallelization turned off. This fix will be included in the v10-01-Public release.

--Bob Y. (talk) 19:31, 2 June 2015 (UTC)

Bob Yantosca followed up:

I have now removed all of the array temporaries. We now copy non-contiguous array slices to temporary arrays, and then pass those temporary arrays to the subroutines MCICA_SUBCOL_LW, MCICA_SUBCOL_SW, RRTMG_LW, RRTMG_SW. This fix will be included in the v10-01-Public release.
NOTE: I tried to use pointer references to avoid having to do explicit array copies, but this caused a segfault in some instances. So I reverted back to the copying of array slabs. This is a robust method and should be safe.

--Bob Y. (talk) 18:24, 3 June 2015 (UTC)

Use org.dat file with OC growth updates

The GEOS-Chem v10-01-Public release will use an updated version of org.dat that includes Randall Martin's updates for better representation of OC growth with RH. For a complete description of the solution, please see this post on our FAST-JX 7.0 photolysis mechanism wiki page.

--Bob Y. (talk) 19:43, 2 June 2015 (UTC)

Update CH4 latitude bands

The last year of latitudinal CH4 concentration data (based on CMDL flask observations) was 2007. (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 2007 thru 2013.

Lee Murray will provide additional latitudinal CH4 concentration data through present day, once it is available. But this update will probably not be ready in time for the v10-01-public release, as it depends on when NOAA releases their updated data product. See this post on our NOx-Ox-HC-aerosol wiki page for more information.

--Melissa Sulprizio (talk) 15:18, 22 May 2015 (UTC)
--Bob Y. (talk) 20:19, 11 June 2015 (UTC)

Flexible precision

At present we are still doing final testing for the flexible precision feature in GEOS-Chem v10-01. We hope to have this ready in the next version, GEOS-Chem v11-01.

--Bob Y. 16:22, 1 May 2015 (EDT)

Adding documentation to describe internal changes made to GMAO met field products

We have created a new wiki page entitled Version history of GMAO met data products, which describes the updates that were made to the various GMAO met data products over time. As of May 2015, the page is under construction. We will be adding more content to the page in the upcoming days.

--Bob Y. 10:45, 6 May 2015 (EDT)'

Minor bug fix in gamap_mod.F

Sebastian Eastham wrote:

On lines 7250-7252 of GeosCore/gamap_mod.F of v10-01 (as downloaded on May 7th or so), the wrong tracer number is referenced when setting MOLC, MWT and SCALE. It currently reads
     7249 | INDEX(T,72) = T + ( SPACING * 72 )
     7250 | MOLC (T,21) = 1
     7251 | MWT  (T,21) = 0e0
     7252 | SCALE(T,21) = 1e0
but presumably it should read as
     7249 | INDEX(T,72) = T + ( SPACING * 72 )
     7250 | MOLC (T,72) = 1
     7251 | MWT  (T,72) = 0e0
     7252 | SCALE(T,72) = 1e0
As a result, the scaling factor, molecular weight and moles of carbon for optical depth (ND21) are all set to 1.0, 0.0 and 0.0. This wouldn’t be a problem except that it leaves the scaling factor for ND72 set to 0.0 – an issue for me because my data reading procedure uses that scaling factor.

--Melissa Sulprizio 15:40, 11 May 2015 (EDT)

Bug fixes for the PGI compiler

We have corrected some minor issues that were preventing GEOS-Chem from compiling with the PGI compiler. For a complete description of the problem, please see this post on our PGI Fortran compiler wiki page.

--Bob Y. 13:07, 13 May 2015 (EDT)

Modifications to Makefile_header.mk

Modifications for netCDF paths

The Makefile_header.mk used in GEOS-Chem v10-01 currently uses these environment variables

GC_BIN        # netCDF bin directory
GC_INCLUDE    # netCDF include directory
GC_LIB        # netCDF library directory

to tell the compiler where to find the netCDF binary, include, and library files. You can set these variables in your .bashrc or .cshrc startup files to point to your system-specific netCDF installation.

But some systems (like the Harvard Odyssey supercomputer) may use a version of netCDF in which the netCDF-Fortran library is installed into a separate data path from the other netCDF library files. To accommodate this type of setup, we have modified the Makefile_header.mk to accept these extra environment variables.

GC_F_BIN      # (NEW!) netCDF-Fortran bin directory
GC_F_INCLUDE  # (NEW!) netCDF-Fortran include directory
GC_F_LIB      # (NEW!) netCDF-Fortran library directory

These variables specifically point to a separate netCDF-Fortran library installation. You can also define these in your .bashrc or .cshrc system startup files, if necessary.

If your netCDF-Fortran library is installed into the same data path as the other netCDF libraries, then you do not need to define GC_F_BIN, GC_F_INCLUDE, and GC_F_LIB. The Makefile_header.mk will now ignore these if they are not defined.

--Bob Y. (talk) 16:27, 21 May 2015 (UTC)

Modifications for KPP chemistry options

In conjunction with our modification to add SOA tracers to the benchmark simulation, we have modified the Makefile_header.mk in order to compile KPP with one of the available GEOS-Chem chemistry mechanisms. This is controlled by the Makefile variable CHEM, as follows:

To pick this mechanism Compile with these options Notes
benchmark make -j4 UCX=y CHEM=benchmark ...
make -j4 ...
  • If you omit CHEM then benchmark will be selected by default.
UCX make -j4 UCX=y CHEM=UCX ...
  • Use with KPP solver.
SOA make -j4 CHEM=SOA ...
  • Can be used with SMVGEAR or KPP
NOx_Ox_HC_Aer_Br
(aka tropchem)
make -j4 CHEM=NOx_Ox_HC_Aer_Br ...
make -j4 CHEM=tropchem ...
  • Formerly known as fullchem
  • Can be used with SMVGEAR or KPP

For more information about these chemistry mechanisms (including a list of tracers in each mechanism), please see:

  1. Appendix 1.1 of the GEOS-Chem Online User's Guide
  2. Chapter 6.1 of the GEOS-Chem Online User's Guide

--Bob Y. (talk) 20:32, 11 June 2015 (UTC)

Fixed typo for BROMOCARB_SEASON in HEMCO configuration files

Luke Schiferl (MIT) pointed out this error. The HEMCO configuration files that shipped with the GEOS-Chem Unit Tester (which are used to create GEOS-Chem run directories) had a typo. The path for the bromocarbon scale factor was incorrect. The incorrect entry was:

# for Bromocarbons:
39 BROMOCARB_SEASON $ROOT/BROMINE/BromoCarb_Season.nc CHXBRY_scale 2000/1-12/1/0 C xy unitless 1

But this should have been:

# for Bromocarbons:
39 BROMOCARB_SEASON $ROOT/BROMINE/v2015-02/BromoCarb_Season.nc CHXBRY_scale 2000/1-12/1/0 C xy unitless 1

We have now fixed all of the relevant HEMCO configuration files in the GEOS-Chem Unit Tester repository. You can pull the change into your local repository with this Git command:

git pull git://git.as.harvard.edu/bmy/GEOS-Chem-UnitTest  v10-01-Release

--Bob Y. 10:51, 13 May 2015 (EDT)

Updates to HEMCO made during the v10-01 period of public comment

Christoph Keller added some updates to HEMCO prior to the release of GEOS-Chem v10-01. Please see this post on our Implementation of HEMCO in GEOS-Chem wiki page for more information.

--Bob Y. 12:30, 13 May 2015 (EDT)

Bug fix in I3 field interpolation

A fix was made in routine INTERP in module GeosCore/dao_mod.F.

Lizzie Lundgren wrote:

TM and TC2, defined as fraction elapsed at timestep mid-point and end, need to be adjusted after the 3hr mark for correct interpolation of I3 fields. Prior to this fix, TM and TC2 span from 0.0 to 2.0 over the 6-hr dynamic timestep when using 3-hour instantaneous data resulting in correct interpolation for hours 0 to 2.75 but incorrect interpolation for hours 3.0 to 5.75. Correct interpolation of 3-hour data requires fractions TM and TC2 to be reset every 3 hours.
The INTERP routine in dao_mod now contains a check for TM > 1.0 if GEOS-FP is defined. If TM > 1.0, then TM and TC2 are reset to TM-1.0 and TC2-1.0. This results in smooth interpolation of I3 fields across the entire dynamic timestep. This bug affects State_Met variables T, SPHU, and PSC2 of GEOS-FP only.
The following lines of code were added to routine INTERP:
   #if   defined( GEOS_FP )
         ! For I3 fields, need to reset fraction after 3 hours (ewl, 5/12/2015)
         IF ( TM > 1.0e+0_fp ) THEN
            TM  = TM  - 1.0e+0_fp
            TC2 = TC2 - 1.0e+0_fp
         ENDIF
   #endif

--Bob Y. 15:32, 13 May 2015 (EDT)

Updated name of ICOADS_SHIP files in HEMCO configuration files

The proper name of the ICOADS_SHIP data files should have been ICOADS.generic.1x1.nc. In the previous HEMCO configuration files, we were using ICOADS.gen.1x1.nc.

ICOADS.gen.1x1.nc is a symbolic link to the file ICOADS.generic.1x1.nc in the HEMCO data subddirectory ICOADS_SHIP/v2014-07/. But some users have reported problems with this symbolic link being copied properly when using the HEMCO data download script. Using the correct file name fixes the problem.

In the HEMCO configuration files that ship with the GEOS-Chem Unit Tester, we changed lines such as:

0  ICOADS_SHIP_CO  $ROOT/ICOADS_SHIP/v2014-07/ICOADS.gen.1x1.nc  CO  2002/1-12/1/0  C xy kg/m2/s CO 6/10 10 1

to:

0  ICOADS_SHIP_CO  $ROOT/ICOADS_SHIP/v2014-07/ICOADS.generic.1x1.nc  CO  2002/1-12/1/0  C xy kg/m2/s CO 6/10 10 1

and etc. for the other ICOADS species.

--Bob Y. (talk) 14:31, 20 May 2015 (UTC)

Avoid PARANOX SUNCOS error by using the proper timestamps

Several GEOS-Chem users have reported encountering this error with the v10-01 provisional release code:

Junwei Xu wrote:

I got an error using v10-01 geos5_2x2.5_soa model for 2012. The error says:
    HEMCO ERROR: LUT error: Fracnox should be between 0 and 1!
    ERROR LOCATION: PARANOX_LUT
I found the exactly same error on wiki, and it says
Christoph Keller updated HEMCO/Extensions/hcox_paranox_mod.F90 to save the correct historic SUNCOS values to the HEMCO restart file.
so I assume the current v10-01 has already implemented these updates. The model indeed worked fine for 2009 & 2010 for me, but crashed with the above error in 2012. Could you please help me work around it?

Temporary fix

NOTE: This "temporary fix" only applies to the v10-01-provisional-release. If you are using the GEOS-Chem v10-01-public-release code, then the permanent fix described below will apply to you.

Each GEOS-Chem run directory that you create from the GEOS-Chem Unit Tester contains a default HEMCO restart file. The file name contains the met field name, horizontal grid and simulation type. (For example, the HEMCO restart file for the GEOS-FP, 4x5, full-chemistry simuation is named initial_hemco_rst.geosfp_4x5.fullchem.nc.) Each HEMCO restart file stores the SUNCOS data fields that are needed to initialize the HEMCO PARANOX extension. The SUNCOS data is usually timestamped with a date such as 2013/07/01 or 2005/01/01, which coinicides with the dates used by most GEOS-Chem unit test simulations.

The corresponding HEMCO_Config.rc file in your run directory contains these lines, which tell HEMCO where to find the HEMCO restart file on disk , and which fields to read from it.

102  PARANOX_SUNCOS1  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS1 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1
102  PARANOX_SUNCOS2  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS2 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1
102  PARANOX_SUNCOS3  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS3 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1
102  PARANOX_SUNCOS4  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS4 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1
102  PARANOX_SUNCOS5  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS5 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1

If the starting date and time of your model simulation does not mach the timestamp of the SUNCOS data in the files, then the C specification in the HEMCO_Config.rc file will instruct HEMCO to read the data block that is closest in time to the current model date and time. For example, if you are running a simulation starting on 2014/01/01 but the SUNCOS data in the HEMCO restart file is timestamped 2013/07/01, then HEMCO will read the data for 2013/07/01.

As we have recently discovered, the HEMCO PARANOX extension is highly sensitive to the date used in the HEMCO restart files. Therefore, if your GEOS-Chem simulation start date does not match the date of the SUNCOS data in the HEMCO restart files, you may get the "Fracnox should be between 0 and 1" error as shown above.

To avoid this issue, you can "cold-reboot" the HEMCO PARANOX extension. If you do not specify that you want to read SUNCOS data from a HEMCO restart file, then the HEMCO PARANOX extension will use default values instead. You can simply comment out the the entries in the HEMCO_Config.rc file by placing a # comment character in front of each line, as shown below:

#102  PARANOX_SUNCOS1  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS1 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1
#102  PARANOX_SUNCOS2  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS2 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1
#102  PARANOX_SUNCOS3  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS3 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1
#102  PARANOX_SUNCOS4  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS4 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1
#102  PARANOX_SUNCOS5  ./initial_hemco_rst.$MET_$RES_fullchem.nc   PARANOX_SUNCOS5 $YYYY/$MM/$DD/$HH  C xy 1 * - 1  1

Permanent fix

Christoph Keller has added this update to HEMCO which fixes the PARANOX SUNCOS issues. It will be added to the v10-01-public release.

--Bob Y. (talk) 21:16, 27 May 2015 (UTC)

Fixes for the 0.25 x 0.3125 nested EU simulation using GEOS-FP meteorology

Anna Protonatariou provided several fixes to allow compilation of GEOS-Chem for the GEOS-FP 0.25° x 0.3125° European nested grid simulation. For more information please see this post on our Nested Model Working Group wiki page.

--Melissa Sulprizio (talk) 21:45, 20 May 2015 (UTC)

Additional fixes for MERRA wet deposition

Carey Friedman originally reported bugs in the calculation of WETLOSS in DO_MERRA_CONVECTION and DO_WASHOUT_ONLY that caused mass of scavenged tracer passed to depo_mercury_mod.F to differ from the mass that is archived in the wet deposition diagnostics (ND38 and ND39). Carey's fixes were implemented in v10-01g. Viral Shah examined these bugs in more detail and proposed several additional bug fixes. For more information, please see this post on our Wet deposition wiki page.

--Melissa Sulprizio (talk) 15:56, 21 May 2015 (UTC)

Minor fixes for FINNv1 biomass burning

For complete information about this issue, please see this post on our FINNv1 biomass burning emissions wiki page.

--Bob Y. (talk) 16:46, 21 May 2015 (UTC)

Resolve issues in the ocean mercury module

We are currently debugging some issues in the ocean mercury module. These were probably introduced when several data files were converted to netCDF so that they could be read via HEMCO. More info to follow shortly. This effort will continue into GEOS-Chem v11-01.

Bob Yantosca also fixed some minor coding issues in the mercury simulation, as described on our Mercury wiki page.

--Bob Y. (talk) 20:38, 11 June 2015 (UTC)

Make TOMAS compatible with HEMCO

We are debugging the TOMAS aerosol microphysics code to make sure that it is compatible with the updates brought in by HEMCO. As of May 22, 2015, we have reached the following milestones:

  1. Seasalt emissions are no
  2. The TOMAS simulation compiles and runs
    • NOTE: More work needs to be done to get it to compile with PRECISION=4
  3. The TOMAS_SeaSalt extension is activated to compute mass and number of sea salt

NOTE: The TOMAS team will have to diagnose this to make sure the output is valid.

--Bob Y. (talk) 22:02, 22 May 2015 (UTC)

Removing additional code made obsolete by HEMCO

We have removed code that was rendered obsolete by the HEMCO emissions component from several routines, including: diag3.F, input_mod.F, ndxx_setup.F, setemdep.F, setemis.F, sulfate_mod.F, tracerid_mod.F, vdiff_mod.F90, vdiff_pre_mod.F90, CMN_O3_mod.F, CMN_SIZE_mod.F, comode_loop_mod.F, carbon_mod.F, gamap_mod.F, seasalt_mod.F, tagged_ox_mod.F, drydep_mod.F.

For a complete list of removed modules, please see our Removal of obsolete modules from GEOS-Chem wiki page.

--Bob Y. (talk) 14:34, 15 June 2015 (UTC)

Add SOA tracers to the GEOS-Chem benchmark simulation

Per request of the GEOS-Chem Steering Committee, we have added the SOA tracers to the GEOS-Chem benchmark simulation. This will now be the default simulation when you run GEOS-Chem "out-of-the box". As a result, we have updated the naming convention for the available GEOS-Chem chemistry mechanisms. We also updated the directory names in the GEOS-Chem Unit Tester accordingly to be consistent with this new naming convention.

For more information, please see the following links:

  1. List of mechanisms for v10-01 on our GEOS-Chem chemistry mechanisms wiki page.
  2. GEOS-Chem Unit Tester
  3. Creating GEOS-Chem run directories
  4. Modifications to Makefile_header.mk for KPP chemistry options
  5. Appendix 1.1 of the GEOS-Chem Online User's Guide
  6. Chapter 6.1 of the GEOS-Chem Online User's Guide

--Bob Y. (talk) 20:03, 11 June 2015 (UTC)

Fix AEFs for sesquiterpenes in the SOA simulation

The sesquiterpene annual emission factors in routine CALC_AEF (in HEMCO/Extensions/hcox_megan_mod.F) needed to be converted from μg compound/m2/hr to kgC/m2/s. This affected the FARN, BCAR, and OSQT species. The missing conversions led to a large decrease in the global mean OH in the 1-month benchmark simulation.

To fix this problem, the following code (in green text) was added to routine CALC_AEF:

     REAL(hp)                :: FACTOR, SPECIES2CARBON

     ...

     ! Conversion factor from [ug compound/m2/hr] to [kg compound/m2/s]
     FACTOR = 1.0e-9_hp / 3600.0_hp
         
     ! Loop over grid boxes
     DO J = 1, HcoState%NY 
     DO I = 1, HcoState%NX

        ! Convert AEF arrays to [kgC/m2/s]
        ! Multiply arrays by FACTOR and ratio [g C/g compound]
        ! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI 
        ! are read from file in [kgC/m2/s], so no need to convert here
        IF ( ExtNrMono > 0 ) THEN
           AEF_APIN(I,J) = AEF_APIN(I,J) 
    &                    * FACTOR * 120.0_hp / 136.234_hp
           AEF_MYRC(I,J) = AEF_MYRC(I,J) 
    &                    * FACTOR * 120.0_hp / 136.234_hp
           AEF_OMON(I,J) = AEF_OMON(I,J) 
    &                    * FACTOR * 120.0_hp / 136.234_hp

           ! Sesquiterpenes
           SPECIES2CARBON = 15.d0 * 12.01d0 / 
    &                     ( 15.d0 * 12.01d0 + 24.d0 * 1.01d0 )
           AEF_FARN(I,J) = AEF_FARN(I,J) * FACTOR * SPECIES2CARBON
           AEF_BCAR(I,J) = AEF_BCAR(I,J) * FACTOR * SPECIES2CARBON
           AEF_OSQT(I,J) = AEF_OSQT(I,J) * FACTOR * SPECIES2CARBON

        ENDIF

--Melissa Sulprizio (talk) 20:11, 11 June 2015 (UTC)

Other miscellaneous updates

In the following HEMCO data files:

  1. UVALBEDO/v2015-03/uvalbedo.geos.2x25.nc
  2. UVALBEDO/v2015-03/uvalbedo.geos.4x5.nc

we changed the unit string of the UVALBD variable from % to percent. We also modified HEMCO accordingly to recognize these units.

Apparently when the % was written to the HEMCO.log file, it was causing Unix to treat the HEMCO.log as a binary file instead of an ASCII file. This issue is now resolved.

You can use the hemco_data_download package to obtain these modified files.

--Bob Y. (talk) 18:37, 16 June 2015 (UTC)

Outstanding issues not yet resolved in GEOS-Chem v10-01

The following issues have not yet been resolved in GEOS-Chem v10-01. Some of these issues represent questions of open research rather than bugs in the source code.

Incorrect photolysis rates in FAST-JX v7.0

Jingqiu Mao (Princeton) and Chris Chan Miller (Harvard) discovered that some FAST-JX v7.0 photolysis rates are incorrect:

  1. Incorrect carbonyl nitrate photolysis rate

This is currently an open area of research in GEOS-Chem.

Incorrect incorporation of moisture in air quantities

This issue was partially resolved in GEOS-Chem v11-01a, which was approved on 07 Jul 2015.

The remaining issue is resolved in GEOS-Chem v11-01h for which benchmarking is in progress.

GCST member Lizzie Lundgren (Harvard) discovered that tracer unit conversions between [v/v] and [kg] do not accurately handle moisture by using moist air mass with dry air molecular weight. Updates to fix this issue and other moisture-related discrepancies discovered during the update implementation were introduced in GEOS-Chem v11-01a.

Validation of the v11-01a moisture corrections revealed an additional moisture handling issue in advection. Inert tracer dry mixing ratio maps contained patterns resembling the moisture signature in the atmosphere. This phenomenon is due to lack of moisture handling within transport. Tracer mass is distributed relative to moist rather than dry air pressure and therefore preferentially pools within grid boxes that contain more water vapor mass.

Meemong Lee and Richard Weidner (JPL) issued a JPL Publication detailing a transport moisture fix for the Adjoint model. Their adjoint fix consists of (1) deriving dry surface pressures from GMAO moist surface pressures and specific humidity, and (2) replacing moist pressures with dry pressures throughout the model.

Lizzie Lundgren (GCST) adapted JPL’s Adjoint fix to the GEOS-Chem forward model in GEOS-Chem v11-01h. The GEOS-Chem implementation (1) corrects the transport mass distribution problem by applying JPL’s fix to transport and unit conversions, (2) preserves the moisture updates incorporated into v11-01a, and (3) preserves inert tracer mass conservation. See the Moisture Updates for v11-01 wiki page for a detailed summary of all of the v11-01a and v11-01g moisture fixes. Changes specific to the updates in v11-01g are discussed in the Transport section.

--Lizzie Lundgren (talk) 15:18, 29 September 2016 (UTC)

Convection mass conservation issue for GEOS-FP

This issue was resolved in GEOS-Chem v11-01a, which was approved on 07 Jul 2015.

Testing of v11-01a revealed a bug in DO_MERRA_CONVECTION that was causing poor mass balance performance. A fix is introduced in v11-01a but can easily be added to v10-01 by users who require improved GEOS-FP convective mass conservation. See the DO_MERRA_CONVECTION bug description on the cloud convection wiki page for how to implement the fix.

--Lizzie Lundgren (talk) 15:08, 25 June 2015 (UTC)
--Bob Y. (talk) 17:43, 7 July 2015 (UTC)

Fix bug in RRTMG that prevents storage of O3 and CH4 RFs

This issue was resolved in GEOS-Chem v11-01a, which was approved on 07 Jul 2015.

David Ridley and Sebastian Eastham fixed an issue in rrtmg_rad_transfer_mod.F that prevented O3 and CH4 RFs from being stored properly. For more information and a description of the bug fix, see this post on our Coupling GEOS-Chem with RRTMG wiki page.

--Melissa Sulprizio (talk) 20:35, 25 June 2015 (UTC)
--Bob Y. (talk) 17:43, 7 July 2015 (UTC)

Bug fix for monoterpenes in ND46 diagnostic

This issue was resolved in GEOS-Chem v11-01c.

Jared Brewer found an issue in the conversion factors used for monoterpenes for the ND46 biogenic emissions diagnostic. For more information, see this post on our MEGAN v2.1 plus Guenther 2012 biogenic emissions wiki page.

--Melissa Sulprizio (talk) 18:45, 9 September 2015 (UTC)

IFORT compiler bugs

Some users have encountered problems with HEMCO that may be caused by compiler bugs in the Intel Fortran Compiler, versions 13, 14, and 15. For more information, see the following wiki posts:

--Melissa Sulprizio (talk) 22:04, 15 September 2015 (UTC)

Out-of-bounds error in mapping_mod II array

A v10-01 patch applied on September 4, 2015 for High-Performance GEOS-Chem introduced a bug in mapping_mod. The bug results in an out-of-bounds error in the 'II' array. The GCST is actively looking into fixing this problem. In the meantime, users who have recently pulled v10-01 source code should revert to the public release version that was committed on June 16, 2015.

--Lizzie Lundgren (talk) 17:33, 18 September 2015 (UTC)

Bug in European grid range for tagged Ox simulation

This update was validated with 1-month benchmark simulation v11-01d and 1-year benchmark simulation v11-01d-Run1. This version was approved on 12 Dec 2015.

There is an error in the European grid definition within tagged_ox_mod.F in v10-01. Please see the tagged ozone simulation wiki page for details.

--Lizzie Lundgren (talk) 14:12, 28 September 2015 (UTC)

Floating point overflow in MERRA/GEOS-FP convection

This update was validated with 1-month benchmark simulation v11-01d and 1-year benchmark simulation v11-01d-Run1. This version was approved on 12 Dec 2015.

Very small values of PDOWN in DO_MERRA_CONVECTION may occur in v10-01 and lead to assorted problems including floating point overflow, high tracer concentrations, and failure of SMVGEAR to converge to a solution. Fixes for this issue have been submitted by Lee Murray and Viral Shah. Lee Murray writes:

We need to add a trap in DO_MERRA_CONVECTION to prevent floating point overflows from occurring when aerosols are potentially re-evaporated. There are times when PDOWN gets small enough (e.g., 2013-11-13, GEOS-FP, 2ºx2.5º, i,j,k = 131,29,14) that it triggers an overflow, ultimately leading the solver to choke.

Viral Shah had previously submitted a fix to be incorporated into v11-01d that corrects this problem. He writes:

I am running v10.01, nested-grid NA full-chemistry w/ SOA simulation with the GEOS-FP met fields, and have found instances of extremely high concentrations of certain tracers that develop all of a sudden...I traced this back to a bug in the DO_MERRA_CONVECTION routine...the value of ALPHA, which should be less than or equal to 1, is sometimes much higher than 1, and for the attached example was >10^5. Since ALPHA is used to calculate resuspension of precipitating mass from above, these high values of ALPHA lead to a gain in tracer mass at the lower levels in excess of what is coming from above.

You may correct this issue in v10-01 by finding the following original code in routine DO_MERRA_CONVECTION within convection_mod.F:

                    ! Define ALPHA, the fraction of raindrops that 
                    ! re-evaporate when falling from (I,J,L+1) to (I,J,L)
                       ALPHA   = ( REEVAPCN(K) * AD(K)          )
    &                            / ( PDOWN(K+1)  * AREA_M2 * 10e+0_fp )

Amend the code to read as follows:

                    ! Define ALPHA, the fraction of raindrops that 
                    ! re-evaporate when falling from (I,J,L+1) to (I,J,L)
                    IF ( PDOWN(K+1) > TINYNUM ) THEN
                       ALPHA   = ( REEVAPCN(K) * AD(K)          )
    &                            / ( PDOWN(K+1)  * AREA_M2 * 10e+0_fp )
                    ELSE
                       ALPHA = 1e+0_fp
                    ENDIF

The fix that will appear in v11-01d is described on the cloud convection wiki page.

--Lizzie Lundgren (talk) 18:17, 29 September 2015 (UTC)

Fix for reading hourly NEI2011 emissions

This update was validated with 1-month benchmark simulation v11-01d and 1-year benchmark simulation v11-01d-Run1. This version was approved on 12 Dec 2015.

Viral Shah wrote:

I have just started using GC v10-01, in more or less an "out of the box" configuration. I am using the NEI 2011 emissions over NA, and found a factor of 2 overestimate in OC concentrations compared to previous model version. It was mainly because of an error in my HEMCO_Config.rc file in the NEI 2011 settings. An example line is below:
      0 NEI11_SURFACE_NO  $ROOT/..nc   NO  2006-2013/1-12/1-31/$HH R xy  kg/m2/s  NO   251/1007     1/2 50
The $HH in the time field was forcing the model to read emissions once daily at 0Z, instead of reading them every hour. I think the $HH should be replaced by 0-23 for them to be read hourly, as the NEI emissions should be.

Christoph Keller wrote:

The $HH flag is misplaced in this context. But I think reading the files every hour slows down the code quite a bit. If you set the hour attribute to the wildcard character HEMCO will read all 24 hour slices at once and pick the currently valid one based on UTC time. This should be more time efficient (but less memory-efficient):
      0 NEI11_SURFACE_NO  $ROOT/..nc   NO  2006-2013/1-12/1-31/* R xy  kg/m2/s  NO   251/1007     1/2 50

--Melissa Sulprizio (talk) 20:21, 21 October 2015 (UTC)

Bug fix for PBLTOP and MTTOP values in tagged ozone simulation

This update was validated with 1-month benchmark simulation v11-01d and 1-year benchmark simulation v11-01d-Run1. This version was approved on 12 Dec 2015.

There is an error in the values set for PBLTOP and MTTOP within routine get_regional_pox in tagged_ox_mod.F. This fix is applicable when using GEOS-5, GEOS-FP, or MERRA. Please see the entry for this fix on the tagged ozone simulation wiki page for details.

Bug fix for offline dust aerosols when UCX is on

This update was validated with 1-month benchmark simulation v11-01d and 1-year benchmark simulation v11-01d-Run1. This version was approved on 12 Dec 2015.

Seb Eastham wrote:

On or around line 1450 of dust_mod.F [in v10-01], the dry radius and extinction of dust are retrieved from QQAA and RDAA. If RRTMG is active, the single scattering albedo and asymmetry factors are also retrieved, from SSAA and ASYMAA. However, they are always read from entry [X,Y,Z,6] of the corresponding array.
Unfortunately, this index is only correct if the UCX is off; if the UCX is on, the entry should be 8, not 6 (based on fast_jx_mod, where these arrays are populated). It looks like an index variable was prepared for this purpose but it's not used. As it is, when the UCX is on, dust radius, surface area and scattering will actually be calculated based on stratospheric sulfate aerosol properties.

--Lizzie Lundgren (talk) 15:51, 23 October 2015 (UTC)

Missing OTD-LIS scale factor for nested Europe

This issue will be corrected in v11-01

Irene Constantina Dedoussi (MIT) reported getting a segmentation fault in the GEOS-5 0.5x0.666 European nested grid simulation, with Err%Loc running out of bounds in HEMCO/Core/hco_error_mod.F90 line 142.

Christoph Keller wrote:

Looks like the problem is that the OTD-LIS scale factor is not properly calculated: whenever HEMCO enters routine Get_OTD_LIS_Scale, it doesn’t leave it properly and the nesting counter keeps increasing. I am not quite sure how this can happen without throwing an error, though. But by looking at subroutine Get_OTD_LIS_Scale in hcox_lightnox_mod.F90, I can see that there are no values for NESTED_EU (only NESTED_CH and NESTED_NA). This will certainly create problems.
For testing, can you try setting the OTD-LIS scale factor explicitly in your HEMCO configuration file? To do so, add the following setting to your lightning NOx extension setup (in HEMCO_Config.rc):
103    LightNOx    : on   NO
         —> OTD-LIS scaling   : 4.375e-2
This is roughly equivalent to the scale factor used for nested NA simulations. Maybe we just forgot to add them to subroutine Get_OTD_LIS_Scale? Either way, we should make sure that the correct values become set in that subroutine.

--Lizzie Lundgren (talk) 22:09, 16 December 2015 (UTC)

Bug fixes for hydrophobic aerosol properties

This update was validated with 1-month benchmark simulation v11-01f and 1-year benchmark simulation v11-01f-geosfp-Run0. This version was approved on 16 Apr 2016.

Seb Eastham identified several bugs setting hydrophobic aerosol properties in aerosol_mod.F, as described on the Mineral Dust wiki page.

--Lizzie Lundgren (talk) 19:23, 5 January 2016 (UTC)

Bug fixes in FINN indexing

This fix will be included in GEOS-Chem_v11-01

Several users reported problems using the HEMCO extension for FINNv1 biomass burning emissions in GEOS-Chem v10-01. Christoph Keller has implemented a fix that will be included in HEMCO v2.0. For more information, see this post on the FINNv1 biomass burning emissions wiki page.

--Melissa Sulprizio (talk) 17:36, 19 May 2016 (UTC)

Cannot compile GEOS-Chem v10-01 with Intel Fortran Compiler v17

This issue is now resolved in GEOS-Chem v11-01.

Compiling GEOS-Chem v10-01 with newer versions of the Intel Fortran Compiler (e.g. ifort 17) results in an error. It appears that OPTIONAL arguments for subroutines included within an INTERFACE block are no longer allowed. The solution to this error is to rewrite the code to remove the offending subroutine arguments.

For a complete description of this issue, please see this post on our Intel Fortran Compiler wiki page.

--Bob Yantosca (talk) 21:01, 20 January 2017 (UTC)