Difference between revisions of "GEOS-Chem v10-01"

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(Bug fix in I3 field interpolation)
(Bug fix in I3 field interpolation)
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:<tt>TM</tt> and <tt>TC2</tt>, defined as fraction of 6h timestep elapsed at mid-point and end of this dynamic timestep, need to be reset after the 3hr mark for the case of I3 fields. Fractions are correct for dynamic timesteps 0 to 2.75 but TM exceeds 1.0 for dynamic timesteps 3.0 to 5.75.
 
:<tt>TM</tt> and <tt>TC2</tt>, defined as fraction of 6h timestep elapsed at mid-point and end of this dynamic timestep, need to be reset after the 3hr mark for the case of I3 fields. Fractions are correct for dynamic timesteps 0 to 2.75 but TM exceeds 1.0 for dynamic timesteps 3.0 to 5.75.
 
      
 
      
:The <tt>INTERP</tt> routine in dao_mod now contains a check for <tt>TM</tt> > 1.0 if [[GEOS-FP]] is defined. If <tt>TM</tt> > 1.0, then <tt>TM</tt> and <tt>TC2</tt> are rest to <tt>TM-1</tt> and <tt>TC2-1</tt>. This results in smooth interpolation of I3 fields across all dynamic timesteps. This bug affects <tt>State_Met</tt> variables <tt>T</tt>, <tt>SPHU</tt>, and <tt>PSC2/tt> of [[GEOS-FP]] only.
+
:The <tt>INTERP</tt> routine in dao_mod now contains a check for <tt>TM</tt> > 1.0 if [[GEOS-FP]] is defined. If <tt>TM</tt> > 1.0, then <tt>TM</tt> and <tt>TC2</tt> are rest to <tt>TM-1</tt> and <tt>TC2-1</tt>. This results in smooth interpolation of I3 fields across all dynamic timesteps. This bug affects <tt>State_Met</tt> variables <tt>T</tt>, <tt>SPHU</tt>, and <tt>PSC2</tt> of [[GEOS-FP]] only.
 
      
 
      
 
:The following lines of code were added to routine <tt>INTERP</tt>:
 
:The following lines of code were added to routine <tt>INTERP</tt>:

Revision as of 19:35, 13 May 2015

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 PROVISIONAL RELEASE 01 May 2015 TBD
View v9-02 benchmark history View v10-01 benchmark history View v11-01 benchmark history

--Bob Y. 09:30, 7 May 2015 (EDT)

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 will last until 15 Jun 2015. During this time, we ask 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 can be implemented.

At the end of the public comment period (15 Jun 2015), if there are no outstanding issues to be resolved, we shall declare GEOS-Chem v10-01 officially released.

--Bob Y. 12:00, 1 May 2015 (EDT)

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 Benchmark approval form for GEOS-Chem 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 Benchmark approval form for GEOS-Chem 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 for complete information about the validation of GEOS-Chem v10-01c:

  1. Approval for 1-month benchmark simulation GEOS-Chem v10-01c
  2. Approval form for 1-year benchmark simulation GEOS-Chem v10-01c Run0
  3. Approval form for 1-year benchmark simulation GEOS-Chem 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 Benchmark approval form for GEOS-Chem 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 Benchmark approval form for GEOS-Chem v10-01e 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 Benchmark approval form for GEOS-Chem 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

Feature Type Submitted by Status
Add fix to prevent a segmentation fault in HEMCO when emissions are turned off Bug fix Christoph Keller (Harvard)
  • As these are all bug fixes, we did not run a benchmark for v10-01g.
  • These will be validated with the v10-01h benchmarks, along with the HEMCO emissions updates.
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 Benchmark approval form for GEOS-Chem v10-01h for complete information about the validation of GEOS-Chem v10-01h.

Feature Type Submitted by Status
FINN 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 Benchmark approval form for GEOS-Chem v10-01i for complete information about the validation of GEOS-Chem v10-01i.

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 lasts from 01 May 2015 to 15 Jun 2015.

Feature Type Submitted by Status
Add more years of latitudinal CH4 data Science Katie Travis (Harvard) In progress
Now use the correct version of FAST-JX input file org.dat Bug fix David Ridley (MIT) " "
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
" "
Fixed typo for BROMOCARB_SEASON in HEMCO configuration files Bug fix Luke Schiferl (MIT)
GEOS-Chem Support Team
" "

--Bob Y. 10:54, 13 May 2015 (EDT)

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.</tt>.
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.

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

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.

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 are currently being resolved during the Period of Public Comment for GEOS-Chem v10-01, which lasts from 01 May 2015 to 15 Jun 2015.

Switching to the officially released GFED4 data files

Prasad Kasibhatla wrote:

Just a quick note.. The current GFED4 emissions in GC are a preliminary version.. The official first version 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)

Technical issues with RRTMG

Bob Yantosca wrote:

There still were a couple more issues 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 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 Y. 16:22, 1 May 2015 (EDT)

Use org.dat file with OC growth updates

We need to 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.

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.

--Melissa Sulprizio 15:53, 11 May 2015 (EDT)

Flexible precision

At present we are still doing final testing for the flexible precision feature in GEOS-Chem v10-01. This should be complete by the end of the public comment period (15 Jun 2015).

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

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

We will update the wiki with some additional information describing the changes made to the GMAO met field data products. In particular, we want to make sure that the GEOS-Chem modeling community is made aware of internal changes made to the current GEOS-FP met data product.

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

Minor bug fix in gamap_mod.F

Sebastian Eastham wrote:

On lines 7250-7252 of 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 compiler wiki page.

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

Modifications to Makefile_header.mk

Bob Yantosca wrote:

In the public comment period for GEOS-Chem v10-01, I modified the Makefile_header.mk so that it now looks for the following variables:
     GC_BIN        # netCDF bin directory
     GC_F_BIN      # netCDF-Fortran bin directory
     GC_INCLUDE    # netCDF include directory

     GC_F_INCLUDE  # (NEW!) netCDF-Fortran include directory
     GC_LIB        # (NEW!) netCDF library directory
     GC_F_LIB      # (NEW!) netCDF-Fortran library directory
On some systems (like the Harvard Odyssey supercomputer), the netCDF C and Fortran libraries may be installed into separate folders on disk (depending on which version of netCDF you use). Therefore I needed to create the GC_F_* environment variables so that I could point to the netCDF-Fortran directory paths.
If your system has the netCDF libraries all in a single path, then in your .cshrc or .bashrc you can simply do this:
     GC_F_LIB=$GC_LIB
     GC_F_INCLUDE=$GC_INCLUDE
     GC_F_BIN=$GC_BIN

--Bob Y. 13:03, 13 May 2015 (EDT)

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 of 6h timestep elapsed at mid-point and end of this dynamic timestep, need to be reset after the 3hr mark for the case of I3 fields. Fractions are correct for dynamic timesteps 0 to 2.75 but TM exceeds 1.0 for dynamic timesteps 3.0 to 5.75.
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 rest to TM-1 and TC2-1. This results in smooth interpolation of I3 fields across all dynamic timesteps. 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)

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.

--Bob Y. 14:09, 13 January 2015 (EST)