GEOS-Chem v9-02

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NOTE: We shall henceforth denote GEOS-Chem versions as GEOS-Chem v9-02, etc. instead of using the previous nomenclature (e.g. GEOS-Chem v9-01-03).

Contents

Overview

In this section we provide basic information about this version of GEOS-Chem.

History

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

Previous version This version Next version
GEOS-Chem v9-01-03 GEOS-Chem v9-02 GEOS-Chem v10-01
PUBLIC RELEASE 14 Sep 2012 PUBLIC RELEASE 03 Mar 2014 PUBLIC RELEASE 17 Jun 2015
View v9-01-03 benchmark history View v9-02 benchmark history View v10-01 benchmark history

--Bob Y. (talk) 20:28, 17 June 2015 (UTC)

Period of public comment

GEOS-Chem v9-02 is the first version of GEOS-Chem for which we issued a PROVISIONAL RELEASE. On 17 Jan 2014, we released the GEOS-Chem source code, data directories, and run directories to the GEOS-Chem User Community. We will then ask the User Community to download and run GEOS-Chem for a period of public comment which lasted until 01 March 2014. During this period of public comment, we encouraged the GEOS-Chem User Community to keep us (the GEOS-Chem Support Team) informed of 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)

Based on the feedback that we received from GEOS-Chem users, we were able to resolve several minor issues mostly involving the specialty simulations and TOMAS simulation.

On 03 Mar 2014, PUBLIC RELEASE was issued for GEOS-Chem v9-02. Subsequent development now continues in GEOS-Chem v10-01.

--Bob Y. 15:51, 3 March 2014 (EST)

What's new in this version

GEOS-Chem v9-02 contains the following major updates and improvements. The order has been determined by the GEOS-Chem Steering Committee.

v9-02a, v9-02b, etc. denote 1-month benchmark simulations, which are designed to evaluate GEOS-Chem's performance at intermediate stages of development.
Alternating stripes of color (white & cyan) in the table below group together features that were evaluated in the same 1-month benchmark.

Feature Type Submitted by Benchmark(s) Status
Correction for GEOS-5 PBL heights Bug Fix Sajeev Philip(Dalhousie) v9-02a Approved 16 Oct 2012
New soil NOx emission module Science Rynda Hudman Kay (EPA)
Neil Moore (formerly of Dalhousie)
Bram Maasakkers (Eindhoven)
v9-02b Approved 29 Oct 2012
Bug fix in hdf_mod.F Bug Fix Sajeev Philip (Dalhousie) " " " "
Bug fixes for tagged CO simulation Bug Fix Jenny Fisher (Wollongong)
GEOS-Chem Support Team
" " " "
Bug fix for nested simulation in nei_anthro_mod.F Bug Fix Sajeev Philip (Dalhousie) " " " "
EPA/NEI05 North American Hg emissions Science Yanxu Zhang (U. Washington)
Lyatt Jaeglé (U. Washington)
v9-02c
+ Hg benchmark (by Hg and POPs Working Group)
Approved 29 Nov 2012
Nested-grid Hg simulation Science Yanxu Zhang (U. Washington)
Lyatt Jaeglé (U. Washington)
" " " "
Streets future Hg emissions Science Bess Corbitt (Harvard) " " " "
Correct Hg simulation to use updated Hg(0) oxidation kinetics Science Bess Corbitt(Harvard)
Justin Parrella (Harvard)
" " " "
Capability to use GEOS-Chem Br/BrO fields in Hg simulation Science Bess Corbitt(Harvard)
Justin Parrella (Harvard)
" " " "
POPs simulation: Polycyclic aromatic hydrocarbons Science Carey Friedman (MIT)
Noelle Selin (MIT)
" " " "
Bug fix for updated CAC emissions Bug Fix Aaron van Donkelaar (Dalhousie) " " " "
Grid-independent GEOS-Chem updates: Activation of new data pathways and other structural modifications Structural GEOS-Chem Support Team v9-02d Approved 19 Dec 2012
Bug fix for Br2 emissions Bug Fix GEOS-Chem Support Team " " " "
Bug fix in regridding of anthropogenic emissions (NEI2005, Streets) Bug Fix GEOS-Chem Support Team v9-02e Approved 09 Jan 2013
Additional bug fixes for MAP_A2A regridding Bug Fix GEOS-Chem Support Team " " " "
Bug fix for MEGAN emissions when using MERRA or GEOS-FP Bug Fix Tzung-May Fu (Peking University) " " " "
Inorganic chemistry updates Science Mat Evans (York) v9-02f
+ 1-year benchmark
1-mon benchmark: Approved 07 Feb 2013
1-year benchmark: Approved 20 Mar 2013
Methyl peroxy nitrate (MPN) chemistry Science Ellie Browne (UC Berkeley) " " " "
Bug fixes for nested Hg simulation Bug fix Yanxu Zhang (U. Washington) " " " "
Prevent bad drydep flux values from being passed to the soil NOx emissions module Bug fix Patrick Kim (Harvard)
GEOS-Chem Support Team
" " " "
Adopt Paulot isoprene scheme as standard Science Fabien Paulot (Harvard)
Eloise Marais (Harvard)
Jingqiu Mao (NOAA/GFDL)
Mat Evans (York)
v9-02g
+ 1-year benchmark
1-mon benchmark: Approved 24 Mar 2013
1-year benchmark: Approved 01 Apr 2013
Fix RO2+HO2 rate constant Science Fabien Paulot (Harvard) " " " "
Increase NO3 uptake by aerosol Science Jingqiu Mao (NOAA/GFDL) " " " "
Bug fix for declaration of GEOS-FP PFICU, PFLCU, PFILSAN, PFLLSAN fields Bug fix GEOS-Chem Support Team " " " "
Bug in EMIS_STREETS_ANTHRO_05x0666 Bug fix Jenny Fisher (U. Wollongong) " " " "
Bug fix for reading OH file in offline simulations Bug fix GEOS-Chem Support Team " " " "
Removal of NOx-Ox partitioning Science GEOS-Chem Support Team v9-02h Approved 15 May 2013
Inhibition of N2O5 uptake by nitrate aerosol Science Lin Zhang (Beijing University) v9-02i Approved 17 May 2013
Improved HO2 uptake by aerosol Science Jingqiu Mao (NOAA/GFDL) v9-02j
+ 1-year benchmark
1-mon benchmark: Approved 28 May 2013
1-year benchmark: Approved 03 Jun 2013
Inline the latest source code modifications updates for the TOMAS microphysics package into GEOS-Chem Structural Sal Farina (CSU)
GEOS-Chem Support Team
v9-02k
+ Hg benchmark
Approved 07 Jun 2013
Hg benchmark pending approval
Additional modifications to enable GEOS-Chem to run within the GEOS-5 GCM Structural GEOS-Chem Support Team " " " "
Streamlining of the code in GeosCore/mercury_mod.F Structural Chris Holmes (UC Irvine) " " " "
Rewriting inefficient subroutine calls to avoid wasting memory and CPU cycles Structural GEOS-Chem Support Team " " " "
Updated NH3 seasonal scaling factors over the US Science Lin Zhang (Peking University) v9-02l
+ 1-year benchmark
1-mon benchmark: Approved 26 Jun 2013
1-year benchmark: Approved 02 Jul 2013
Updated Canadian NH3 inventory Science Wai-Ho Lo (Dalhousie) " " " "
Bug in wet deposition Henry's constant Bug fix Fabien Paulot " " " "
Add DRYACET to globchem.dat Bug fix Emily Fischer (Harvard) " " " "
Fix diurnal NOx scale factors and fix double counting of biofuels over Mexico, Canada, and Europe Bug Fix Christoph Keller (Harvard) " " " "
Bug fix for 3-hourly GFED3 emissions Bug fix Christoph Keller (Harvard) " " " "
Bug fix in grid_mod.F90 Bug Fix Christoph Keller (Harvard) " " " "
Bug fix for anthropogenic scaling factors for years 2006 and later Bug fix Jenny Fisher (U. Wollongong) " " " "
Correct additional bugs in ship emissions w/ non-local PBL mixing Bug Fix Chris Holmes (UC Irvine)
Geert Vinken (Eindhoven)
" " " "
Bug fix for ship CO emissions Bug Fix Chris Holmes (UC Irvine) " " " "
Fix typo in VOLCPRESS definition Bug fix Thibaud Thonat (U. Edinburgh) " " " "
Eliminate several more array temporaries Structural GEOS-Chem Support Team " " " "
Bug fixes in day-of-week computation Bug fix GEOS-Chem Support Team " " " "
Bug fixes in diag48_mod.F Bug fix Jenny Fisher (U. Wollongong) " " " "
Bug fix in emissions for offline aerosol simulation Bug fix GEOS-Chem Support Team " " " "
RCP emission scenarios Science Chris Holmes (UC Irvine) v9-02m
+ CH4 benchmark (by Carbon Gases & Organics WG)
1-mon benchmark: Approved 30 Jul 2013
EDGAR v4.2 emissions for CH4 simulation Science Kevin Wecht (Harvard) " " " "
Update anthropogenic scale factors through 2010 Science Aaron van Donkelaar (Dalhousie) " " " "
Update GFED3 emissions to 2011 Science Prasad Kasibhatla (Duke) " " " "
Update TOMS overhead O3 columns to 2010 Science Jenny Fisher (U. Wollongong) " " " "
Include 12-bin and 15-bin configurations of TOMAS Science Sal Farina (CSU) " " " "
Corrected minor bugs for GCAP that were introduced by GIGC edits Bug fix GEOS-Chem Support Team " " " "
Prevent negative emissions over Canada Bug fix Fabien Paulot (Harvard)
Christoph Keller (Harvard)
" " " "
AEIC aircraft emissions inventory Science Sebastian Eastham (MIT)
Steven Barrett (MIT)
v9-02n Approved 12 Aug 2013
SOA simulation with semi-volatile POA Science Havala Pye (EPA)
GEOS-Chem Support Team
v9-02o Approved 03 Sep 2013
Implement non-local PBL mixing in the Rn-Pb-Be simulation Science Jintai Lin (Peking University)
GEOS-Chem Support Team
" " " "
Minor bug fix in TOMAS sulfate emissions Bug fix Sal Farina (CSU) " " " "
Bug fix in ND36 diagnostic when ship emissions are turned off Bug fix Yanko Davila (U. Colorado) " " " "
Initial modifications for GEOS-Chem Unit Tester Structural GEOS-Chem Support Team " " " "
Cloud water pH for sulfate formation Science Becky Alexander (U. Washington) v9-02p Approved 13 Sep 2013
Fix molecular weights of RIP and IEPOX used in drydep_mod.F Bug fix GEOS-Chem Support Team " " " "
Bug fixes to prevent floating-point invalid errors Bug fix GEOS-Chem Support Team " " " "
Update jv_spec.dat and jv_spec_aod.dat with better representation of OC growth with RH and correction to sulfate optics Science David Ridley (MIT)

Randall Martin (Dalhousie)

v9-02q Approved 17 Sep 2013
Bug fix in jv_spec_aod.dat for dust species Bug fix Gabriele Curci (U. L'Aquila) " " " "
Nested-grid model at 0.25° x 0.3125° resolution using GEOS-5 "FP" met data product from GMAO Structural Yuxuan Wang (Tsinghua)
GEOS-Chem Support Team
v9-02r
+ Rn-Pb-Be benchmark
+ Nested-grid benchmark (by Nested Model WG)
1-mon benchmarks: Approved 14 Dec 2013

1-year benchmarks: Approved 14 Jan 2014

High-resolution emissions for above nested-grid model Science Yuxuan Wang (Tsinghua)
GEOS-Chem Support Team
" " " "
Global simulations with GEOS-5 "FP" data product from GMAO
(Needed for the 0.25° x 0.3125° nested-grid simulations)
Structural GEOS-Chem Support Team " " " "
Additional minor bug fixes Bug fix GEOS-Chem Support Team " " " "
Fix bug in CAC NH3 emission files Bug fix Wai Ho Lo (Dalhousie) " " " "
Update molecular weight of sea salt tracers Science Colette Heald (MIT) " " " "
Bug fix for NEI2005 SO4 emissions in sulfate_mod.F Bug fix Jenny Fisher (U. Wollongong) " " " "
Add unit tester capability (i.e. to automatically compile GEOS-Chem for all met fields/grid combinations in order to spot common errors) Structural GEOS-Chem Support Team Now in place as an external package 22 Aug 2013
ISSUES RESOLVED DURING THE PUBLIC COMMENT PERIOD
Updates for the CH4 simulation: Bug fix &
Structural
Kevin Wecht (Harvard) Last-minute fix
Reactivate stratospheric P(Ox) in tagged Ox simulation Bug fix Jintai Lin (Peking University) Last-minute fix
Replace LD65 with LLTROP in tagged_ox_mod.F Bug fix Hongyu Liu (NIA/NASA Langley) Last-minute fix
Fixes for TOMAS aerosol microphysics Bug fix Sal Farina
Jeff Pierce (CSU)
GEOS-Chem Support Team
Last-minute fix
Corrected unit conversion bug when TURBDAY PBL mixing is used Bug fix Sebastian Eastham (MIT)
GEOS-Chem Support Team
Last-minute fix
Fixes for minor technical issues Bug fix Lee Murray (LDEO)
GEOS-Chem Support Team
Last-minute fix
Prevent error in POPs simulation when reading global OC data Bug fix Ka Ming Wai (CUHK)
GEOS-Chem Support Team
Last-minute fix
Updated comments to better reflect the grassroots nature of GEOS-Chem Structural Colette Heald (MIT)
GEOS-Chem Support Team
Last-minute fix
Prevent 0.5 x 0.667 nested grid simulations from crashing when reading TOMS data Bug fix Luke Schiferl
GEOS-Chem Support Team
Last-minute fix
Clean up several modules that use the Meteorology State object Structural GEOS-Chem Support Team Last-minute fix
POST-RELEASE PATCHES
Fix bug in acetone photolysis pressure dependency Bug fix Sebastian Eastham (MIT) Post-release patch

--Melissa Sulprizio 16:15, 22 May 2014 (EDT)

Downloading and installing GEOS-Chem v9-02

For complete instructions on how to download and install GEOS-Chem v9-02, please visit the following links:

--Bob Y. 10:11, 16 January 2014 (EST)

New data directories

The following new data directories have been added for GEOS-Chem v9-02. You will have to download the directories relevant to your simulation.

You can download these directories with anonymous FTP or the Wget utility. For instructions, please see Chapter 2.4, Downloading the GEOS-Chem shared data directories in the GEOS-Chem Online User's Guide.

GEOS_0.25x0.3125_CH                    # Met fields and emissions for 0.25° x 0.3125° nested CH simulation
 
GEOS_0.25x0.3125_NA                    # Met fields and emissions for 0.25° x 0.3125° nested NA simulation

GEOS_0.5x0.666_NA/CAC_201307           # Canadian NH3 emissions
GEOS_0.5x0.666_NA/CH4_201305           # EDGAR v4.2 emissions for CH4 simulation
GEOS_0.5x0.666_NA/RETRO_201103         # RETRO anthropogenic VOC emissions
GEOS_0.5x0.666_NA/RCP_201206           # RCP future emission scenarios
GEOS_0.5x0.666_NA/lightning_NOx_201311 # Lightning redistribution files
GEOS_0.5x0.666_NA/mercury_201203       # Data files for the nested NA Hg simulation

GEOS_0.5x0.666_CH/RETRO_201103         # RETRO anthropogenic VOC emissions (0.5° x 0.667° CH nested grid)

GEOS_0.5x0.666_EU/RETRO_201103         # RETRO anthropogenic VOC emissions( 0.5° x 0.667° NA nested grid)

GEOS_2x2.5/CH4_201305                  # EDGAR v4.2 emissions for CH4 simulation
GEOS_2x2.5/GEOS_FP                     # GEOS-FP meteorology fields
GEOS_2x2.5/POPs_201209                 # BC & OC concentrations for POPs simulation
GEOS_2x2.5/RCP_201206                  # RCP future emission scenarios
GEOS_2x2.5/lightning_NOx_201311        # Lightning redistribution files
GEOS_2x2.5/mercury_201203              # NEI2005 and NPRI2005 emissions for Hg simulation

GEOS_4x5/CH4_201305                    # EDGAR v4.2 emissions for CH4 simulation
GEOS_4x5/GEOS_FP                       # GEOS-FP meteorology fields
GEOS_4x5/POPs_201209                   # BC & OC concentrations for POPs simulation
GEOS_4x5/RCP_201206                    # RCP future emission scenarios
GEOS_4x5/lightning_NOx_201311          # Lightning redistribution files
GEOS_4x5/mercury_201203                # NEI2005 and NPRI2005 emissions for Hg simulation

GEOS_NATIVE/AEIC_201301                # AEIC aircraft emissions
GEOS_NATIVE/CAC_201307                 # Canadian NH3 emissions
GEOS_NATIVE/CH4_201402                 # CH4 emissions at 0.25 x 0.3125 NA grid
GEOS_NATIVE/GFED3_201212               # GFED3 emissions, now including 2011
GEOS_NATIVE/POPs_201209                # BaP, PHE, and PYR emissions for POPs simulation
GEOS_NATIVE/mercury_201205             # Streets future anthropogenic Hg emissions
GEOS_NATIVE/soil_NOx_201208            # Files for updated soil NOx emission scheme
GEOS_NATIVE/TOMAS_201402               # Large data files for TOMAS aerosol microphysics

--Bob Y. 11:06, 24 February 2014 (EST)

Using the GEOS-Chem Unit Tester

We now have a new tool that you can use to help debug your GEOS-Chem simulations! The GEOS-Chem Unit Tester can now run short test simulations designed to reveal several common programming and/or numerical issues, including:

  1. Parallelization errors
  2. Array-out-of-bounds errors
  3. Division-by-zero errors
  4. Invalid computations (i.e. SQRT(-1), LOG(0), etc.)
  5. Inefficient subroutine calls.

For more information about how the GEOS-Chem Unit Tester can help your debugging efforts, please see our Debugging with the GEOS-Chem unit tester wiki page.

--Bob Y. 12:15, 16 January 2014 (EST)

Validation

In this section we provide information about the benchmarks and tests that we have done to validate GEOS-Chem v9-02.

1-month and 1-year benchmarks

We have performed several 1-month and 1-year benchmarks in order to validate the code updates for GEOS-Chem v9-02. For complete information, please see our GEOS-Chem v9-02 benchmark history wiki page.

--Bob Y. 10:07, 27 February 2014 (EST)

Unit test matrix for GEOS-Chem v9-02

The matrix below displays the results of several unit tests (performed with the GEOS-Chem Unit Tester) for the GEOS-Chem v9-02 public release. Each unit test validates a particular combination of met field, horizontal grid, and simulation type (e.g. GEOS-5 met + 4° x 5° grid + fullchem simuation, etc.).

In the table below:

  • GREEN denotes a successful unit test
  • YELLOW denotes that the unit test revealed an issue in that needs to be investigated further
  • RED denotes an unsuccessful unit test
  • WHITE denotes that a unit test was not performed for the given combination of met fields & grid.


Met Fields Grid Fullchem SOA SOA w/ SVPOA Hg Rn-Pb-Be TagO3 CH4 CO2 TOMAS40
GEOS-FP 4° x 5°
MERRA 4° x 5°
GEOS-5 4° x 5°
GEOS-5 2° x 2.5°
GEOS-4 4° x 5°
GCAP 4° x 5°

NOTES:

  1. For more information on the issue with the TOMAS simulation, please see this wiki post.
  2. To see the results file from the unit test simulations shown above, please follow this link.
  3. The GCAP simulation passed the normal unit test simulation (1 hour simulation). Subsequent testing (> 3 hour simulations) revealed a potential numerical issue when soil NOx emissions are activated. We are continuing to look at this issue and hope to have a fix for GEOS-Chem v10-01.

--Bob Y. 15:45, 3 March 2014 (EST)

Validating the changes made since the provisional release

During the period of public comment (Jan 17 thru Mar 1, 2014) following the provisional release of GEOS-Chem v9-02, several GEOS-Chem users notified us of minor issues that needed to be corrected. We used a method known as difference testing to validate these updates.

List of commits made during the public comment period

In order to fix the minor issues identified by the user community, we made several new commits to the GEOS-Chem Git repository. Each commit represents a new update made to the GEOS-Chem source code. The table below shows all of the commits that were made during this period:

Commit ID# Date Description Category
a7622ff 26 Feb 2014 Clean up use of State_Met in several modules
(LATEST UPDATES)
Structural fix
666c3f5 26 Feb 2014 Prevent 0.5x0.666 nested simulations from crashing in toms_mod.F Nested-grid fix
1b66757 25 Feb 2014 Update modules in GeosApm with last-minute fixes for v9-02 Structural fix
3e94259 25 Feb 2014 Added ProTex headers to a6_read_mod.F and i6_read_mod.F Structural fix
dc1b3d3 25 Feb 2014 Replace title at top of ProteX headers Structural fix
7c65298 24 Feb 2014 Prevent error in POPs simulation when reading global OC Specialty simulation fix
9b50b32 21 Feb 2014 Fix for parallelization in TOMAS wet scavenging TOMAS simulation fix
65b5204 20 Feb 2014 Remove some debug print for TOMAS in drydep_mod.F TOMAS simulation fix
970541d 18 Feb 2014 removed attempt at saving solfrac in subroutine do_rainout_only TOMAS simulation fix
c8be713 18 Feb 2014 Fixed logical errors that prevented dust emissions in TOMAS. TOMAS simulation fix
311c742 19 Feb 2014 Additional minor updates for 0.25 x 0.3125 NA CH4 simulation Specialty simulation fix
c6f6311 13 Feb 2014 Use DATA_DIR instead of DATA_DIR_1x1 for CH4 sim at 0.25 x 0.3125 NA grid Specialty simulation fix
0374734 12 Feb 2014 Add 0.25 x 0.3125 NA nested grid capability to CH4 simulation Specialty simulation fix
0d65395 04 Feb 2014 Bug fix for ND37, ND38 diagnostics in convection_mod.F TOMAS simulation fix
211aa52 04 Feb 2014 Now place ND37 diagnostic update in same loop as COMPUTE_F TOMAS simulation fix
ccf74ba 03 Feb 2014 Remove obsolete references to TINDEX, TCOUNT, TMAX Technical fix
d00bbf3 03 Feb 2014 BugFix: TOMAS wetdep is different for serial/parallel computing TOMAS simulation fix
162611e 03 Feb 2014 Add linoz_mod.o to dependency list for input_mod.o Technical fix
185328e 31 Jan 2014 Now read TOMAS data files from shared disk space TOMAS simulation fix
1294b11 31 Jan 2014 Avoid parallelization error in drydep_mod.F for TOMAS simulations TOMAS simulation fix
50addef 31 Jan 2014 Bug fix: eliminate typo in input_mod.F TOMAS simulation fix
a87707a 31 Jan 2014 Bug fix: Now save out tracerinfo.dat properly for ND44 diag w/ TOMAS TOMAS simulation fix
81fb282 31 Jan 2014 TOMAS bug fix: Add missing variables to !$OMP+PRIVATE statement TOMAS simulation fix
746cc79 29 Jan 2014 Fixed bug in call to SET_CH3Br, SET_BrO for TURBDAY PBL mixing Technical fix
11a1758 29 Jan 2014 Avoid array temporaries in TOMAS simulations, update #3 TOMAS simulation fix
23cd1d1 29 Jan 2014 Avoid out-of-bounds error for ND44 diagnostic w/ TOMAS simulations TOMAS simulation fix
0d35b34 28 Jan 2014 Avoid array temporaries in TOMAS simulations, update #2 TOMAS simulation fix
babeb85 28 Jan 2014 Avoid array temporaries in TOMAS simulations, update #1 TOMAS simulation fix
871f460 28 Jan 2014 Corrected minor numerical issues for TOMAS simuations TOMAS simulation fix
5c29e2e 27 Jan 2014 Now do a CALL FLUSH(6) in main.F when using TOMAS TOMAS simulation fix
d51a2fe 27 Jan 2014 Add tomas_mod.o to the dependency list for wetscav_mod.o. TOMAS simulation fix
81cbc8b 23 Jan 2014 Replace LD65 and LLTROP_FIX with LLTROP in tagged_ox_mod.F TOMAS simulation fix
a013beb 23 Jan 2014 Reactivate call to ADD_STRAT_POX in tagged Ox simulation Specialty simulation fix
03ebdb2 23 Jan 2014 Fixes for wetland emissions in CH4 simulation Specialty simulation fix
faace49 15 Jan 2014 Merge branch 'lightning' into Dev
(PROVISIONAL RELEASE 17 Jan 2014)

As you can see, most of these issues pertained to the GEOS-Chem specialty simulations (e.g. CH4, Tagged Ox, POPs) or to the TOMAS aerosol microphysics simulations. None of these issues affected the standard full-chemistry or SOA simulations.

Difference tests

In order to ensure that all of these fixes and updates did not affect the full-chemistry simulations, we have performed quick difference tests. A difference test is a short simulation where we compare the output of a reference code to a development code. The reference code represents the last trusted benchmarked version, and the development code contains several additional updates that we wish to verify.

In order to validate all of the updates made to GEOS-Chem since the provisional release of 17 Jan 2014, we performed the following difference tests:

Test # Reference Code Development Code Result
1
  • GEOS-Chem Provisional Release (commit ID# faace49)
  • GEOS-FP meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation w/ non-local PBL mixing
  • 1 day (2012/07/01 to 2012/07/02)
  • GEOS-Chem Latest Updates (commit ID# a7622ff)
  • GEOS-FP meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation w/ non-local PBL mixing
  • 1 day (2012/07/01 to 2012/07/02)
IDENTICAL
2
  • GEOS-Chem Provisional Release (commit ID# faace49)
  • MERRA meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation w/ non-local PBL mixing
  • 1 day (2005/07/01 to 2005/07/02)
  • GEOS-Chem Latest Updates (commit ID# a7622ff)
  • MERRA meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation w/ non-local PBL mixing
  • 1 day (2005/07/01 to 2005/07/02)
IDENTICAL
3
  • GEOS-Chem Provisional Release (commit ID# faace49)
  • GEOS-5 meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation
  • 1 day (2012/07/01 to 2012/07/02)
  • GEOS-Chem Latest Updates (commit ID# a7622ff)
  • GEOS-5 meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation
  • 1 day (2012/07/01 to 2012/07/02)
IDENTICAL
4
  • GEOS-Chem Provisional Release (commit ID# faace49)
  • GEOS-4 meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation + full PBL mixing
  • 1 day (2005/07/01 to 2005/07/02)
  • GEOS-Chem Latest Updates (commit ID# a7622ff)
  • GEOS-4 meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation + full PBL mixing
  • 1 day (2005/07/01 to 2005/07/02)
DIFFERENT
5
  • GEOS-Chem Provisional Release (commit ID# faace49)
  • GEOS-4 meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation + full PBL mixing
  • 1 day (2005/07/01 to 2005/07/02)
  • + commit 746cc79 (Fixed bug in call to SET_CH3Br, SET_BrO for TURBDAY PBL mixing)
  • GEOS-Chem Latest Updates (commit ID# a7622ff)
  • GEOS-4 meteorology
  • 4° x 5° horizontal grid
  • Full-chemistry simulation + full PBL mixing
  • 1 day (2005/07/01 to 2005/07/02)
IDENTICAL

--Bob Y. 16:39, 28 February 2014 (EST)

Interpreting the results

We may draw the following conclusions from the results of the above difference tests:

  1. For the GEOS-FP, MERRA, and GEOS-5 met fields (Tests #1, #2, #3), we obtained identical results in all cases. This gives us confidence to say that all of the updates that were added in between the GEOS-Chem v9-02 provisional release and the GEOS-Chem v9-02 public release do not negatively impact the full-chemistry simulation.

  2. We attribute the DIFFERENT results in the GEOS-4 test (Test #4) to this particular commit:

    746cc79 Fixed bug in call to SET_CH3Br, SET_BrO for TURBDAY PBL mixing
    Because this commit introduced a fix that applies to simulations using TURBDAY (full PBL mixing), all GEOS-4 full-chemistry simulations are affected. For this reason, the development code could not replicate the results of the reference code. When we add the commit #746cc79 to the Reference Code and re-run the test (Test #5), then we obtain identical results.

--Bob Y. 11:01, 28 February 2014 (EST)

Performance

In this section we provide information about the GEOS-Chem's scalability. This is best illustrated as a plot of GEOS-Chem run times as you increase the number of CPUs on your system.

Scalability of the standard 1-month benchmark simulation

Mat Evans wrote:

I've run lots of the benchmark version (4x5 geos5 1 month) with different numbers of cores for GEOS-Chem v9-01-03 and v9-02. I've run this all on a 2CPU Xeon X5670 @ 2.93GHz which has 6 cores per chip. 12 cores per system and up 24 threads through the hyper threading.
Speedup v9-02.png

Bob Yantosca wrote:

I think a couple of things were responsible for the speedup:
  1. We removed a lot of array temporaries from the code. In particular, this was happening in the TPCORE routines—the code had to make duplicate copies several IIPAR x JJPAR x LLPAR arrays for each subroutine call. And this was done in a loop over N = 1, 66 tracers, so you can imagine the bottleneck that was being created.
  2. We just re-activated the parallel DO loop in the LINOZ module. Some time ago this was reported as problematic. But I tested it again recently and found that it worked OK. This will increase the scalability for runs where we call chemistry several times an hour (i.e. 2x25, nested grids), since the fraction of code that is parallelized is greater than before.
In our recent GEOS-Chem v9-02r 1-month benchmark (GEOS-5, 4x5) benchmark run, we got about 730% speedup on 8 CPUs (800% is theoretical max). That’s pretty good. The I/O is still all on single processor so you really can’t do better there.
Also … I am not sure how well OpenMP parallelization performs with hyperthreading (where 1 CPU acts as if it were 2 CPUs). That may explain the falloff that you see when you go past 12 CPUs. On 12 or less CPUs, you are using the actual # of CPUs/node. But when you go past 12 CPUs, and into hyperthreading, you probably incur some additional system overhead, and that could be causing the turnover in the graph.

--Bob Y. 10:51, 19 November 2013 (EST)

Scalability of GEOS-Chem with GEOS-FP meteorology

It should be noted that GEOS-Chem simulations using GEOS-FP meteorology scale slightly lower than equivalent simulations using GEOS-5 meteorology. This can be illustrated by looking at the timing results from these two 1-month benchmarks:

Benchmark # of CPUs Run time Scalability
v9-02r 1-month benchmark w/ GEOS-5 met 8 2h 38min 7.2794
v9-02r 1-month benchmark w/ GEOS-FP met 8 2h 47min 6.9529


A "perfect" simulation using 8 CPUs would theoretically have a scalability of 8.0000. In practice, we never attain the ideal scalability due to the following factors:

  1. As you use more CPUs in a simulation, each CPU has to communicate with the others more frequently). This incurs additional system overhead.
  2. Some sections of GEOS-Chem have not been parallelized. This is particularly true of the sections of code which handle file I/O.

As you can see from the above table, GEOS-Chem simulations using GEOS-FP met scale slightly worse than when using GEOS-5 met. We believe that this can be explained by:

  1. GEOS-FP requires more frequent reading of data from disk than GEOS-5.
    • GEOS-5 meteorology needs to be read at intervals of 3 hours (surface fields) and 6 hours (3-D fields).
    • GEOS-FP meteorology needs to be read at intervals of 1 hour (surface fields) and 3 hours (3-D fields).
  2. GEOS-FP uses a different file format than GEOS-5.
    • GEOS-5 meteorology is archived as flat binary files, which are very quick to read in.
    • GEOS-FP meteorology is saved in netCDF files. Reading netCDF files requires a call to the netCDF library routines, which incurs additional overhead.

--Bob Y. 11:31, 16 January 2014 (EST)

Previous issues now resolved in GEOS-Chem v9-02

This section contains a list of improvements and bug fixes that have been included in GEOS-Chem v9-02. For a complete list of bug fixes in GEOS-Chem, please see our Bugs and fixes wiki page.

Correction for GEOS-5 PBL heights

This update was tested in the 1-month benchmark simulation v9-02a and approved on 16 Oct 2012.

Please see this post on our Boundary layer mixing wiki page for a full description of this issue.

--Bob Y. 11:01, 5 October 2012 (EDT)

Bug fixes for tagged CO simulation

This update was tested in the 1-month benchmark simulation v9-02b and approved on 29 Oct 2012.

Please see this post on our Tagged CO simulation wiki page for more a complete description of the issue.

--Bob Y. 10:59, 20 December 2012 (EST)

Bug fix in nei2005_anthro_mod.F

This update was tested in the 1-month benchmark simulation v9-02b and approved on 29 Oct 2012.

This code was removed from GEOS-Chem v10-01 and higher versions. All emissions are now handled by HEMCO.

We corrected incorrect subroutine calls to the regridding subroutine DO_REGRID_A2A from routines GET_NEI99_SEASON_05x0666 and GET_VISTAS_SEASON_05x0666 of GeosCore/nei2005_anthro_mod.F. Please see this wiki post on our EPA/NEI05 North American emissions wiki page for further information.

--Bob Y. 11:13, 20 December 2012 (EST)

Bug fix for updated CAC emissions

This update was tested in the 1-month benchmark simulation v9-02c and approved on 29 Nov 2012.

This code was removed from GEOS-Chem v10-01 and higher versions. All emissions are now handled by HEMCO.

Aaron van Donkelaar wrote:

The code as implemented in v9-01-03 contains only few of the changes I submitted to update CAC to 2008. My guess is that somehow two versions of this file were being worked on simultaneously.
As a result of the mix-up, simulations using CAC emissions and running 2006 or 2007 will crash. Other than that it shouldn't have had any major ramifications.

--Melissa Payer 15:51, 27 November 2012 (EST)

Bug fix for Br2 emissions

This update was tested in the 1-month benchmark simulation v9-02d and approved on 19 Dec 2012.

This code was removed from GEOS-Chem v10-01 and higher versions. All emissions are now handled by HEMCO.

Please see this wiki post on our Bromine Chemistry Mechanism wiki page for a full description of this issue.

--Bob Y. 15:38, 20 December 2012 (EST)

Bug in regridding of anthropogenic emissions

NOTE: This issue was tested in the 1-month benchmark simulation in v9-02e, which was approved on 09 Jan 2013.

We corrected an issue in the regridding of the anthropogenic Streets and NEI2005 emissions. Please see the discussion on our Regridding in GEOS-Chem wiki page for more information.

--Bob Y. 10:21, 10 January 2013 (EST)

Bug in MEGAN emissions when running with MERRA or GEOS-FP

NOTE: This issue was tested in the 1-month benchmark simulation in v9-02e, which was approved on 09 Jan 2013.

This code was removed from GEOS-Chem v10-01 and higher versions. All emissions are now handled by HEMCO.

Please see the discussion on our MEGAN biogenic emissions wiki page for a complete description of this issue.

--Bob Y. 10:34, 10 January 2013 (EST)

Additional bug fixes for MAP_A2A regridding algorithm

NOTE: This issue was tested in the 1-month benchmark simulation v9-02e, which was approved on 09 Jan 2013.

Please see the discussion on our Regridding in GEOS-Chem wiki page for a complete description of this issue.

--Bob Y. 10:25, 10 January 2013 (EST)

Prevent bad drydep flux values from being passed to the soil NOx emissions module

This issue was tested in the 1-year benchmark simulation v9-02f and approved on 20 Mar 2013.

In GEOS-Chem v10-01 and higher versions, soil NOx emissions are now handled by HEMCO.

It was discovered that junk values in the drydep fluxes were being passed to the soil NOx emissions module (via routine SOIL_DRYDEP) when the ND44 dry deposition diagnostic was switched off. We have now corrected this issue. Please see this post on our Soil NOx emissions wiki page for more information.

--Bob Y. 09:29, 14 March 2013 (EDT)

Bug fix for declaration of GEOS-FP PFICU, PFLCU, PFILSAN, PFLLSAN fields

This update was tested in the 1-month benchmark simulation v9-02g and approved on 24 Mar 2013.

Please see this wiki post on our GEOS-FP implementation details wiki page for a full description of this issue.

--Bob Y. 11:42, 18 March 2013 (EDT)

Bug fix for reading OH file in offline simulations

This update was tested in the 1-month benchmark simulation v9-02g and approved on 14 Mar 2013.

This module was removed from GEOS-Chem v10-01 and higher versions. Oxidants now read from disk via the HEMCO emissions component.

When running the nested grid simulation over North America, a segmentation fault would occur in routine GET_GLOBAL_OH. GEOS-Chem was previously reading the global 0.5x0.666 data file, which lead to an array-out-of-bounds error. To make sure that the proper file is read, the following lines have been added to routine GET_GLOBAL_OH in GeosCore/global_oh_mod.F:

#if defined( NESTED_NA )
      ! Filename
      FILENAME = TRIM( OH_DIR ) // 'OH_3Dglobal.' // GET_NAME_EXT() // 
     &           '.'            // GET_RES_EXT()  // '_NA'
#else
      ! Filename
      FILENAME = TRIM( OH_DIR ) // 'OH_3Dglobal.' // GET_NAME_EXT() // 
     &                              '.'           // GET_RES_EXT()
#endif

--Melissa Sulprizio 14:40, 6 September 2013 (EDT)
--Bob Yantosca (talk) 15:44, 11 January 2016 (UTC)

Bug fixes in biofuel_mod.F and emfossil.F

This update was tested in the 1-month benchmark simulation v9-02l and approved on 26 Jun 2013. This update is included in Adjoint v34j.

Modules biofuel_mod.F and emfossil.F were GEOS-Chem v10-01 and newer versions. Anthropogenic and biofuel emissions are now implemented via the HEMCO emissions component.

Christoph Keller wrote:

I found two bugs in the emissions code which I think we should fix.
Firstly, the diurnal NOx scale factors should be based on local time instead of Greenwich Mean Time (aka Universal Time). The fix is easy, we just have to use the local time for a given grid box instead of taking the UTC hour when calculating the emissions in GeosCore/emfossil.F.
Secondly, I think that we currently double count biofuel emissions over Canada and Mexico if the respective local inventories (CAC and BRAVO) are used. Again, this is an easy fix, we just have to set the biofuel emissions for the given tracers and regions to zero if CAC and/or BRAVO are used.

Christoph Keller wrote:

After having had a second look at the EMEP data I'm pretty sure that they contain biofuel emissions too. So I will have to update GeosCore/biofuel_mod.F accordingly, then it should be ready to merge.

--Melissa Payer 18:21, 20 June 2013 (EDT)
--Bob Yantosca (talk) 15:45, 11 January 2016 (UTC)

Bug in wet deposition Henry's constant

This update was tested in the 1-month benchmark simulation v9-02l and approved on 26 Jun 2013.

This update was removed in GEOS-Chem v11-01e. The wet deposition module wetscav_mod.F now uses routines from GeosUtil/henry_mod.F to compute the liquid/gas Henry's law coefficient. This will ensure that Henry's law computations are done consistently throughout GEOS-Chem.

Fabien Paulot found a small bug in Henry's constant used in the wet deposition routine. Please see this post on our Wet deposition wiki page for a full description of this issue.

--Melissa Payer 17:58, 15 May 2013 (EDT)
--Bob Yantosca (talk) 15:49, 11 January 2016 (UTC)

Bug fix for anthropogenic scaling factors for years 2006 and later

This update was tested in the 1-month benchmark simulation v9-02l and approved on 26 Jun 2013.

Module scale_anthro_mod.F was removed from GEOS-Chem v10-01 and newer versions. Anthropogenic scale factors are now implemented via HEMCO.

Please see this post on our Scale factors for anthropogenic emissions wiki page for a full description of this issue. We plan to include this fix in GEOS-Chem v9-02n.

--Melissa Payer 12:25, 22 March 2013 (EDT)
--Bob Yantosca (talk) 15:48, 11 January 2016 (UTC)

Bug in ship CO emissions

This update was tested in the 1-month benchmark simulation v9-02l and approved on 26 Jun 2013.

Module emfossil.F has been removed from GEOS-Chem v10-01 and newer versions. EMEP ship emissions are now implemented via the HEMCO emissions component.

Please see this post on our Ship Emissions wiki page for a full description of the issue. We plan to include this fix in GEOS-Chem v9-02m.

--Bob Y. 15:47, 8 April 2013 (EDT)
--Bob Yantosca (talk) 15:47, 11 January 2016 (UTC)

Bug fixes in day-of-week computation

This update was tested in the 1-month benchmark simulation v9-02l and approved on 26 Jun 2013.

In GEOS-Chem v10-01 and higher versions, local time offsets for emissions are now handled by HEMCO.

We corrected a couple of issues regarding how the day of the week is computed in GEOS-Chem. We made this fix primarily to ensure EPA/NEI weekday or weekend emissions were being selected properly. The EPA/NEI emissions are defined over the United States, where the local solar time can be 5-8 hours behind Greenwich Mean Time. Therefore, when deciding if EPA/NEI weekday or weekend emissions should be applied, we should use the day of the week w/r/t the local time at each grid box location over the United States. But in all GEOS-Chem versions prior to v9-02, the day of the week was always computed w/r/t Greenwich Mean Time.

In order to correct this discrepancy, we made the following modifications in GEOS-Chem v9-02l:

(1) We have now moved the location of where the day of the week (w/r/t the GMT date) is computed:
  • Subroutine SET_CURRENT_TIME (in GeosUtil/time_mod.F) computes the day of the week and stores it in module variable DAY_OF_WEEK.
  • Function GET_DAY_OF_WEEK (also in GeosUtil/time_mod.F) now just returns the value of module variable DAY_OF_WEEK to the calling program.
(2) We fixed a couple of numerical issues in the computation of the day of the week (w/r/t the GMT date), namely:
(a) In subroutine SET_CURRENT_TIME (in module GeosUtil/time_mod.F), we need to round off the B term to 4 decimal places in order to avoid roundoff errors. We added this line:
          ! NOTE: This is not in the Duffett-Smith book, but when using
          ! REAL*8, we have to round B to 4 decimal places in order
          ! to avoid floating-point errors. (bmy, 6/13/13)
          B           = INT( NINT( B*1d5 + SIGN( 5d0, B ) ) / 10d0 ) / 1d4
(b) Also in SET_CURRENT_TIME, we changed the line:
          DAY_NUM = INT( B + 0.5d0 )
to
          DAY_NUM = INT( B )
The extra 0.5 was causing the day of week to increment 12 hours ahead of time. (The 0.5 is present in the algorithm upon which the function is based. But since this algorithm was developed for hand-held calculators, it may not take into account the roundoff that may exist in floating point numerical computations.)
(3) Note that as written, subroutine SET_CURRENT_TIME returns the day of the week with respect to the Greenwich Mean Time (GMT). But when deciding to apply either weekday or weekend emissions at a particular location on the globe, we really want to get the day of the week with respect to the local solar time at that location. The local solar time may differ from GMT by several hours depending on distance from the prime meridian. Therefore, we have introduced a new function named GET_DAY_OF_WEEK_LT, which computes the day of the week with respect to the local time at a given location. Emissions routines that need to know the day of the week shall now use GET_DAY_OF_WEEK_LT instead of GET_DAY_OF_WEEK.
(a) In the following emissions modules:
  • GeosCore/biofuel_mod.F
  • GeosCore/emfossil.F
  • GeosCore/epa_nei_mod.F
  • GeosCore/nei2005_anthro_mod.F
  • GeosCore/sulfate_mod.F
  • GeosCore/vistas_anthro_mod.F
we have added code to call the new function GET_DAY_OF_WEEK_LT, in order to obtain the day of the week w/r/t the local solar time at GEOS-Chem grid box (I,J,L). The typical pattern that we use is as follows:
               REAL*8  :: DOW_LT
               LOGICAL :: WEEKDAY

               . . .

               DO J = 1, JJPAR
               DO I = 1, IIPAR

                  ! Determine if we should use weekday or weekend NEI
                  ! emissions at grid box (I,J,L).  Since NEI is over
                  ! the US, then weekend is Sat/Sun.
                  DOW_LT       = GET_DAY_OF_WEEK_LT( I, J, 1 )
                  WEEKDAY      = ( DOW_LT > 0 .and. DOW_LT < 6 )
 
                  ! Call emissions routines (in this example, EPA/NEI99)
                  AN           = GET_EPA_ANTHRO(  I, J, IDTSO2, WEEKDAY )
                  BF           = GET_EPA_BIOFUEL( I, J, ITDSO2, WEEKDAY )

                  ... etc ...

               ENDDO
               ENDDO
Important notes:
  • Sunday is denoted when DOW_LT == 0, and Saturday is denoted when DOW_LT == 6. For the purposes of the EPA/NEI emissions (over the United States), a "weekend" is Saturday/Sunday. (NOTE: in some locations of the world, particularly in the Middle East, weekends are defined as Friday/Saturday.)
  • We now need to call GET_DAY_OF_WEEK_LT from the same DO loop where the call to the emissions routines (in this example, for EPA/NEI99) are located. This is because GET_DAY_OF_WEEK_LT now needs to know the I, J, (and for multi-level data, L) indices of the grid box.
  • If the DO loop is parallelized, then the variables DOW_LT and WEEKDAY need to be added to the !$OMP PRIVATE declaration.

--Bob Y. 14:27, 18 June 2013 (EDT)

Bug fixes in diag48_mod.F

This update was tested in the 1-month benchmark simulation v9-02l and approved on 26 Jun 2013.

NOTE: We are phasing out binary punch diagnostics output GEOS-Chem v11-01, in favor of netCDF output.

Jenny Fisher wrote:

A couple of bugs in diag48_mod.F:
1. GET_LOCALTIME is called with LT = GET_LOCALTIME( I, J, L )
But L hasn't been defined. This should either be K or 1, but not L.
2.
          DO L = 1, K
             Q(L) = GET_PEDGE( I, J, K )
          ENDDO
The K in GET_PEDGE should be L.

--Melissa Payer 14:36, 18 June 2013 (EDT)

Bug in ND36 diagnostic when ship emissions are turned off

This update was tested in the 1-month benchmark simulation v9-02o and approved on 03 Sep 2013.

NOTE: We are phasing out binary punch diagnostics output GEOS-Chem v11-01, in favor of netCDF output.

For a full description of this issue, please see this post on our Ship emissions wiki page.

--Melissa Sulprizio 11:36, 22 August 2013 (EDT)

Additional minor bug fixes

These updates were tested in the 1-month benchmark simulation v9-02r and approved on 14 Nov 2013.

These issues were mainly identified with the GEOS-Chem Unit Tester while validating GEOS_Chem v9-02r.

  1. Do not call PARANOX when running offline simulations
  2. Make sure BC and OC biofuel emissions are zeroed out when using the RCP emission scenarios (submitted by Colette Heald)
  3. Fixed parallelization error in routine METERO (in dry deposition module)
  4. Fixed parallelization error in routine DRYFLX (in dry deposition module)
  5. Eliminate array temporaries in GEOS-4 convection module
  6. Prevent LOG(0) error from occurring in soil NOx module
  7. Eliminate array temporaries in GCAP convection module
  8. Eliminate array temporaries in pjc_pfix_mod.F and pressure_mod.F
  9. Avoid error in ISOROPIAII when using offline aerosol simulation
  10. Modifications for v9-02 tagged O3 simulation
  11. Reactivate parallel DO loop in LINOZ_CHEMO3 routine
  12. Reset NaNs in MOISTQ to zero
  13. Bug fix for RCP ship NOx emissions

--Bob Y. 15:01, 7 November 2013 (EST)

Use reprocessed data files for CAC NH3 emissions

This update was tested in the 1-month benchmark simulation v9-02r and approved on 14 Nov 2013.

In GEOS-Chem v10-01 and higher versions, CAC emissions are read from disk via the HEMCO emissions component.

The 1-year benchmark for v9-02l revealed that Canadian NH3 emissions were not varying with season as expected. Wai Ho Lo has reprocessed the data files for the CAC NH3 emissions. These new emission files are slated for inclusion in v9-02r. For more information please see this post on our Anthropogenic emissions wiki page.

--Bob Y. 16:36, 31 October 2013 (EDT)
--Bob Yantosca (talk) 15:47, 11 January 2016 (UTC)

Convert MERRA and GEOS-FP relative humidity fields to percent after reading from disk

This update was tested in 1-month benchmark simulation v9-02r with GEOS-FP met and approved on 14 Jan 2014.

Aaron van Donkelaar wrote:

I've noticed some oddities in the surface-layer relative humidity of a MERRA-driven simulation, as output from diag51. The attached plot shows the RH output in the lowest two layers of a GEOS-5- and MERRA-driven simulation for Aug 27, 2005 using v9-01-03.
MERRA RH avd.jpg
A couple things jump out. First, MERRA RH goes from 0-1, rather than 0-100, and second, the lowest layer (shown in the bottom left) is really noisy.
The simulation was run by another user, whom is checking into it as well. I was, however, wondering if this was something you had already come across and could maybe shed some light on.

Bob Yantosca replied:

It appears we read in GEOS-5 RH as unitless then convert to %. It seems be that we do not do this unit conversion for MERRA (or for GEOS-FP).


Older met products (e.g. GEOS-1, GEOS-STRAT, GEOS-4) carried RH with units of %. The newer GMAO met products all carry RH as unitless. Therefore, for backwards compatibility with existing GEOS-Chem code, we have to convert RH to % immediately after reading it in from disk. This unit conversion is done when running GEOS-Chem with GEOS-5 met. But as you can see from the above plot, this unit conversion currently does not happen when running GEOS-Chem with either MERRA or GEOS-FP met.

This issue can be resolved by adding a couple extra lines of code:

1. In GeosCore/merra_i3_mod.F, we modify the CASE statement for RH to add the unit conversion:

            !------------------------------------
            ! RH: Relative humidity [1]
            !     and converted to  [%]
            !------------------------------------
            CASE ( 'RH' )
               READ( IU_I6, IOSTAT=IOS ) XYMD, XHMS, Q3
               IF ( IOS /= 0 ) CALL IOERROR( IOS, IU_I6, 'read_i6:3' )

               IF ( XYMD == NYMD .and. XHMS == NHMS ) THEN
                  CALL TRANSFER_3D( Q3, RH )
                  NFOUND = NFOUND + 1 

                  ! Convert RH from [1] to [%] 
                  RH = RH * 100d0
               ENDIF

2. In GeosCore/geosfp_read_mod.F90, we add the same unit conversion in the last section of the routine (just before exiting):

    !======================================================================
    ! Unit conversions, diagnostics, cleanup, and quit
    !======================================================================
    
    ! Convert RH from [1] to [%]
    State_Met%RH = State_Met%RH * 100d0

    ! CLDTOPS = highest location of CMFMC in the column (I,J)
    DO J = 1, JJPAR
    DO I = 1, IIPAR
    ... etc ...

3. For consistency, we have also updated the comments in Headers/gigc_state_met_mod.F90 to reflect the proper units:

     REAL*8,  POINTER :: RH        (:,:,:)  ! Relative humidity [%]
     REAL*8,  POINTER :: RH1       (:,:,:)  ! RH at timestep start [%]
     REAL*8,  POINTER :: RH2       (:,:,:)  ! RH at timestep end [%]	

These fixes correct the issue. The diagnostics now report RH in %, as seen by the following plot.

Fixed rh.jpg

These updates have since been added to GEOS-Chem v9-02.

--Bob Y. 10:44, 16 January 2014 (EST)

Bug fix for NEI2005 SO4 emissions in sulfate_mod.F

This update was included as a last-minute fix in GEOS-Chem v9-02 and approved on 14 Jan 2014.

This code was removed from GEOS-Chem v10-01 and higher versions. All emissions are now handled by HEMCO.

Please see this post on our EPA/NEI05 North American emissions wiki page for more a complete description of the issue.

--Bob Y. 10:45, 16 January 2014 (EST)

Issues resolved during the public comment period

The following issues were brought to our attention by the GEOS-Chem users during the public comment period (17 Jan 2014 thru 01 Mar 2014) following the provisional release of GEOS-Chem v9-02. These items were fixed prior to the official release of GEOS-Chem (03 Mar 2014).

Updates for the CH4 simulation

We have added several minor fixes for the CH4 simulation in GEOS-Chem v9-02.

Fixes for wetland emissions in CH4 simulation

This adds a couple of minor fixes to the CH4 simulation which were never included into the standard GEOS-Chem code. For a full description, please see this post on our CH4 simulation wiki page.

--Bob Y. 16:49, 23 January 2014 (EST)

Add support for GEOS-FP 0.25 x 0.3125 NA nested grid

Kevin Wecht has supplied the new emissions files on the 0.25° x 0.3125° NA (North America) nested grid for the CH4 simulation. These are now stored in the directory GEOS_NATIVE/CH4_201402. We have added the corresponding changes to the source code in global_ch4_mod.F.

--Bob Y. 11:35, 12 February 2014 (EST)

Turn off CH4_BUDGET diagnostic by default

In order to save memory, we now turn off the CH4_BUDGET diagnostic by default in the CH4 simulation. If you would like to restore this diagnostic, you can remove the ! comment symbol in front of this line of code at the top of GeosCore/global_ch4_mod.F:

!#define USE_CH4_BUDGET_DIAG 1

If you are using the CH4 simulation at the 0.25° x 0.3125° resolution, you will want to leave the CH4 BUDGET diagnostic disabled. This will help to save memory.

--Bob Y. 11:35, 12 February 2014 (EST)

Reactivate stratospheric P(Ox) in tagged Ox simulation

We have implemented a fix that had been submitted to us but not yet added into the standard GEOS-Chem. This issue only affected the tagged Ox simulation. For a full description, please see this post on our Tagged Ox simulation wiki page.

--Bob Y. 16:49, 23 January 2014 (EST)

Replace LD65 with LLTROP in tagged_ox_mod.F

We have implemented a fix that had been submitted to us but not yet added into the standard GEOS-Chem. This issue only affected the tagged Ox simulation. For a full description, please see this post on our Tagged Ox simulation wiki page.

--Bob Y. 16:49, 23 January 2014 (EST)

Fixes for TOMAS microphysics

Using the GEOS-Chem Unit Tester, we have found and fixed several minor issues for the TOMAS aerosol microphysics simulation. These fixes were included in the public release of GEOS-Chem v9-02 (03 Mar 2014). For more information, please see this post on our TOMAS aerosol microphysics wiki page.

--Bob Y. 16:35, 13 May 2014 (EDT)

Corrected unit conversion bug when TURBDAY PBL mixing is used

We have corrected a unit conversion error that caused the concentrations of CH3Br (and also BrO, if you have selected the option to fix BrO to 1 pptv in input.geos) when the TURBDAY (full PBL) mixing scheme is used. For more information, please see this post on our Boundary layer mixing wiki page.

--Bob Y. 10:37, 5 February 2014 (EST)

Fixes for minor technical issues

We have now issued last-minute fixes for these minor technical issues:

  1. In routine READ_DIAGNOSTIC_MENU (in GeosCore/input_mod.F), we have removed the USE statements referencing the TINDEX, TCOUNT, and TMAX from module GeosCore/diag_mod.F. These were erroneous statements; these variables are instead included in Headers/CMN_DIAG_mod.F.. Lee Murray reported that these obsolete references caused GEOS-Chem compilation to choke on Macintosh platforms.

  2. We had omitted linoz_mod.o from the dependency list to input_mod.o in GeosCore/Makefile. This is because we call INIT_LINOZ from routine GIGC_Init_Extra. This is now corrected.

--Bob Y. 10:37, 5 February 2014 (EST)

Prevent error in POPs simulation when reading global OC data

This code was removed from GEOS-Chem v10-01 and higher versions. All emissions are now handled by HEMCO.

We have fixed an error which caused a segmentation fault in the POPs simulation. The error occurred when the GEOS-Chem was trying to read organic carbon (OC) data beyond the last data year of 2009. For a complete description of this fix, please see when reading global OC data this post on our POPs simulation wiki page.

--Bob Y. 12:08, 24 February 2014 (EST)

Updated comments to better reflect the grassroots nature of GEOS-Chem

Colette Heald wrote:

I was doing my Introduction-to-GEOS-Chem spiel with an undergrad today and showing him how to compile the code and he asked me about this at the top of all the sub-routines:
   !------------------------------------------------------------------------------
   !          Harvard University Atmospheric Chemistry Modeling Group            !
   !------------------------------------------------------------------------------
I had just explained to him how GEOS-Chem is a grass-roots model that really benefits from the efforts of scientists around the world, and obviously this labeling seemed antithetical to that....
I realize this is purely historical baggage, and in the past most of the community had a direct tie to Harvard, but in this era where many more groups are participating in the development and management of the model, I wondered if we could replace this in the code with something like GEOS-Chem Global Chemical Transport Model?

Bob Yantosca replied::

That is an easy fix. We can do that before the public release of v9-02.

--Bob Y. 16:40, 25 February 2014 (EST)

Prevent 0.5 x 0.667 nested grid simulations from crashing when reading TOMS data

We have added a fix for the 0.5 x 0.667 nested grid simulations so that TOMS O3 columns are read from the older TOMS_200906 data directory. For a complete description of this fix, please see this post on our FAST-J photolysis mechanism wiki page.

--Melissa Sulprizio 10:40, 26 February 2014 (EST)

Clean up several modules that use the Meteorology State object

We have cleaned up several modules that use the State_Met derived type object in an attempt to make the code more readable. This update will also help to reduce the number of conflicts that arise when bringing in new features that are based on older versions of GEOS-Chem. For a complete description, please see this post on our Derived type objects used by the Grid-Independent GEOS-Chem wiki page.

--Melissa Sulprizio 17:59, 27 February 2014 (EST)

Post-release patches

The following updates were added as bug fix patches after the public release of GEOS-Chem v9-02 (03 Mar 2013):

v9-02 post-release patch to fix error in acetone photolysis

We have prepared a post-release patch for GEOS-Chem v9-02 in order to correct an issue in the acetone pressure dependency for FAST-J photolysis. This error was not discovered at the time of the v9-02 public release on 03 Mar 2014. For complete information about this issue (and how to apply the patch), please see this post on our FAST-J photolysis mechanism wiki page.

--Bob Y. 15:33, 27 May 2014 (EDT)

Outstanding issues not yet resolved in GEOS-Chem v9-02

The following issues have not yet been resolved in GEOS-Chem v9-02. For a complete list of unresolved issues by GEOS-Chem version, please see our Currently unresolved issues in GEOS-Chem wiki page.

Regional biofuel emissions may be neglected when using RETRO or RCP emissions

This issue was resolved with the addition of the HEMCO emissions component into GEOS-Chem v10-01. The prior emissions code has now been removed from GEOS-Chem.

For a complete description of this issue, please see this post on our Biofuel emissions wiki page. NOTE: This issue will likely be resolved when the new HEMCO emissions component is implemented into GEOS-Chem.

--Bob Y. 12:13, 5 February 2014 (EST)

Isoprene emissions are lower when using GEOS-FP meteorology

It has been noted that the GEOS-FP 1-year benchmark runs produce much less isoprene than the GEOS-5 1-year benchmark run. This is not a necessarily a problem with the model, but is a matter of active research.

Dylan Millet wrote:

Indeed isoprene emissions are now quite low, dropping to 395 TgC/y with GEOS-FP and further to 361 TgC/y once we also use the Olson 2001 land map. 361 TgC is 409 Tg isoprene, this puts us at the low end of other estimates using MEGAN2.1 which are mostly 500-600 Tg/y. (But not totally outside the range)
Overall CO seems to have decreased overall, but the change appears not as dramatic as previously when the anthro emissions were also different.
My feeling is we shouldn't scale isoprene emissions for their own sake, since as far as I know it's an open science question as to whether 500-600 Tg/y is a better global estimate than 400. But, if a consensus emerges among the SC that the low isoprene causes too much of a step-change in other species like CO and PAN, then that would be grounds for scaling.
I will forward this discussion on to other folks who have been involved in MEGAN development in GC and see what their thoughts are.

Daniel Jacob replied:

It seems to me that the GEOS-FP run is OK. There are large differences with GEOS-5 but nothing that seems to obviously compromise the quality of the model and the rest is a matter of research. Dylan M thinks that we should live with the lower isoprene at least for the time being. I suggest that we approve this version and go on to [the next version].

--Bob Y. 10:56, 16 January 2014 (EST)

Soil NOx issues with GEOS-FP meteorology

In GEOS-Chem v10-01 and higher versions, soil NOx emissions are now handled by HEMCO.

In the course of our benchmarking the standard simulation with GEOS-FP meteorology, we have noted a couple of issues relating to the soil NOx emissions.

Soil NOx emissions are lower when using GEOS-FP meteorology

The lower surface temperatures in GEOS-FP (as described in the preceding section also cause soil NOx emissions to be lower compared to GEOS-5. Again, this does not necessarily indicate a problem with GEOS-Chem, but is also a matter of active research.

Prasad Kasibhatla wrote:

Is there an obvious exp;anation for why the NO soil and fertilizer sources have decreased by about 20% in 1-year benchmark v9-02-geosfp-Run0 relative to v9-02-geos5-Run0? Is it because of surface temperature?

Daniel Jacob replied:

Thanks Prasad. 20% decrease in NOx soil source is very consistent with the cooler temperatures in GEOS-FP driving the isoprene decrease. I don't think that needs to be investigated further.

--Bob Y. 11:06, 16 January 2014 (EST)

Need to adjust pulsing threshold when using GEOS-FP meteorology

Patrick Kim added:

In the course of our SEAC4RS-related research, we noted that the soil NOx emissions at 4° x 5° exhibits pulsing behavior that is sometimes inconsistent with the 0.25° x 0.3125° simulation. After looking at the implementation, Karen Yu has discovered that this is likely because the threshold for a pulsing event to occur is a constant (that was actually determined for a 0.5 degree resolution grid), whereas it should probably be resolution-dependent. A fix for the standard code will be issued, likely in GEOS-Chem v10-01.

--Bob Y. 16:33, 23 January 2014 (EST)

Ozone in eastern US is too high when using the Olson 2001 land map

This update was validated in the 1-month benchmark simulation v10-01a and approved on 05 Feb 2014.

It was discovered that ozone in the eastern US in GEOS-Chem v9-02 was too high when using the Olson 2001 land map. The Olson 2001 land map is currently the default setting when using the GEOS-FP met fields.

UPDATE: Patrick Kim implemented the following updates to correct this issue. These updates were NOT be included into the public release of GEOS-Chem v9-02, but into GEOS-Chem v10-01a.

--Bob Y. 16:36, 13 May 2014 (EDT)

Potential parallelization problem in TOMAS diagnostics

We have noticed that there may be a parallelization error in the TOMAS ND60 diagnostic. For a full description of this issue, please see this post on our TOMAS aerosol microphysics wiki page.

--Bob Y. 16:22, 21 February 2014 (EST)

O3 completely removed at Shanghai grid box with GEOS-FP 4x5 simulation

This issue was resolved with the addition of the HEMCO emissions component into GEOS-Chem v10-01. To resolve this issue, Chris Holmes supplied an update for PARANOX, which was implemented as a HEMCO extension.

Patrick Kim and Bob Yantosca have noticed that compiling and running GEOS-Chem with the following options:

make -j4 MET=geosfp GRID=4x5 DEBUG=yes FPE=yes

caused all of the ozone to be titrated out of grid box (I=61, J=31, L=1) on date 2013/01/01. It appears that the ozone is being removed due to excessive ozone deposition. (Recall that a negative ozone production efficiency from the PARANOX ship plume model will be treated as an ozone loss via dry deposition.) In particular, this condition can be exacerbated in grid boxes that have very high anthropogenic NO concentrations, but are close to the ocean.

Patrick Kim wrote:

Something that I didn't realize: the box (61,3,1) that we are talking about is mostly a land box and contains Shanghai. I think a factor that is leading to zero ozone (and thus the mutli-fold increase in ship O3 deposition since we divide by surface ozone concentration in the SHIPO3DEP array) actually has to do with the anthropogenic sources leading to O3 titration once the sun goes down and the PBL gets lower. I think this may be a unique case where we have a large NO point source in a large grid box that overlaps the ocean.
My reasoning behind this is that SHIPO3DEP modifies the ozone deposition if there is ozone depletion in the ship plume, but it doesn't really make sense to have ozone loss if there is no ozone left in the box anyway. So as long as we have the error trap for when ozone is set to SMAL2=1d-99, we just roll with having zero ozone in the box (and the titration makes sense when and where it occurs). This shouldn't be a problem at higher resolutions.

If you should encounter a similar error, then try omitting the FPE=yes and DEBUG=yes flags during GEOS-Chem compilation. We will keep an eye on this issue.

Update 7/17/14: Chris Holmes provided a fix for this issue. For a complete description of the fix, please see this post on the Ship emissions wiki page.

--Bob Y. 17:01, 25 February 2014 (EST)

Potential issue with soil NOx in GCAP simulation

As of 03 Mar 2014, we are still investigating a potential issue with the GCAP simulation that seems to be related to soil NOx emissions. Runs longer than 1 hour exhibited different results at the (single processor vs/ multi processor) when the soil NOx emissions were activated. We are continuing to look into this issue, and hope to have a fix for GEOS-Chem v10-01.

--Bob Y. 15:36, 3 March 2014 (EST)

Incorrect 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.

NOTE: In GEOS-Chem v11-01 all species molecular weights will be defined centrally in the GEOS-Chem species database.

Jenny Fisher noted that the molecular weight (g/mol) of the PROPNN tracer had been listed incorrectly in the input.geos files that shipped w/ GEOS-Chem v9-02. The incorrect value was 109 g/mol, as shown in this line of input.geos:

Tracer #57              :  57   PROPNN 109.0   PROPNN

But the correct value should have been 119 g/mol:

Tracer #57              :  57   PROPNN 119.0   PROPNN

This error affects full-chemistry, SOA, and aerosol microphysics simulations. We will fix this in the next version (GEOS-Chem v10-01), as this update will require a benchmark simulation. In the meantime, please feel free to update your input.geos files accordingly.

--Bob Y. 14:23, 4 March 2014 (EST)

Timeseries diagnostics need to be updated to allow for more transported tracers

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

NOTE: We are phasing out binary punch diagnostics output in GEOS-Chem v11-01, in favor of netCDF output.

Prasad Kasibhatla wrote:

Re the ND49, 50, 51, and 51b diagnostics - I think the code needs to be updated to allow for more than 75 transported tracers because the SOA simulation has 93 tracers. Currently, indices 76 and higher are used for quantities other than transported tracers.

We will fix this issue in GEOS-Chem v10-01, but users of GEOS-Chem v9-02 should be aware of the problem and note that some of the timeseries diagnostic quantities may not save out properly when using the SOA simulation.

In v10-01c, we implemented a fix so that indices 1-150 in the timeseries diagnostics are reserved for GEOS-Chem tracers and 151-200 are used for the additional diagnostic quantities. The pure O3, NO, and NO2 concentration options have been removed because O3, NO, and NO2 are now tracers (see this post on the removal of NOx and Ox partitioning update implemented in 1-month benchmark simulation v9-02h).

--Melissa Sulprizio 11:13, 7 March 2014 (EST)

Bug in 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.

It was discovered after the GEOS-Chem v9-02 public release that Input_Opt%USE_O3_FROM_MET might not be set properly for simulations using GEOS-5 meteorology, so TOMS O3 columns might not be used as expected. Please see this post on our FAST-J photolysis mechanism wiki page for more information.

--Melissa Sulprizio 12:24, 11 March 2014 (EDT)

Parallelization error in nested grid simulations

This update was validated in the 1-month benchmark simulation v10-01d and approved on 03 Jun 2014.

Jintai Lin reported differences in nested grid simulation output when using the GEOS-Chem Unit Tester. For a full description of this issue and its solution, please see this wiki post on our GEOS-Chem nested grid simulations wiki page.

--Melissa Sulprizio 17:36, 10 March 2014 (EDT)

Missing error checks for RCP in input_mod.F

This issue was resolved by the addition of the HEMCO emissions component into GEOS-Chem v10-01.

The following code has been removed from GEOS-Chem. HEMCO has now rendered the previous emissions routines obsolete.

Jenny Fisher wrote:

I've just noticed that v9-02 at least is missing error checks in input_mod.F for RCP emissions, including RCP aircraft and ship emissions. The way this is set currently, if e.g. LRCP=T but emissions (or anthro emissions) are turned off, LRCP will remain true which will cause downstream problems later.
This can be fixed by adding the following to input_mod.F (new lines in bold):
     LARCSHIP          = ( LARCSHIP       .and. LANTHRO   )
     LCOOKE            = ( LCOOKE         .and. LANTHRO   )
     LRCP              = ( LRCP           .and. LANTHRO   )
     LRCPAIR           = ( LRCPAIR        .and. LANTHRO   )
     LRCPSHIP          = ( LRCPSHIP       .and. LANTHRO   )

     ! Biogenic
     LMEGAN            = ( LMEGAN         .and. LBIOGENIC )

--Melissa Sulprizio 09:35, 9 June 2014 (EDT)

Bug fixes and updates for tagged CO in v9-02

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

Jenny Fisher found several bugs and inconsistencies in the tagged CO simulation in GEOS-Chem v9-02. For a full description of these issues and their solutions, please see this post on our Tagged CO simulation wiki page.

--Melissa Sulprizio 09:31, 10 July 2014 (EDT)
--Bob Y. 18:29, 13 January 2015 (EST)

Avoid segmentation faults when starting simulations at times other than 00 UTC

This issue was resolved by the addition of the HEMCO emissions component into GEOS-Chem v10-01.

The following code has been removed from GEOS-Chem. HEMCO has now rendered the previous emissions routines obsolete.

Chris Holmes wrote:

I am trying to debug in GEOS-Chem and want to start simulations at times other than 00 UTC. I am using v9-02.
When starting at 20060101 010000, I get seg faults and other errors because emission arrays have not been allocated. Apparently GC is not running all of the initialization subroutines. First, I found that "BRAVO_MASK" is not allocated. I then turned off BRAVO emissions and found that "SO2_SHIP" is not allocated.

To resolve this problem, we suggest adding a first-time flag to routine DO_EMISSIONS (found in GeosCore/emissions_mod.F)

     LOGICAL, SAVE :: FIRST = .TRUE.

and modifying the IF statements for BRAVO and SO2 ARCTAS emissions as follows:

        ! Read BRAVO (Mexico) emissions once per year
        IF ( LBRAVO .and. ( FIRST .or. ITS_A_NEW_YEAR() ) ) THEN
           CALL EMISS_BRAVO( am_I_Root, Input_Opt, State_Chm, RC )
        ENDIF

        ...

        ! Read SO2 ARCTAS emissions
        IF ( LARCSHIP .AND. ( FIRST .or. ITS_A_NEW_YEAR() ) ) THEN
           CALL EMISS_ARCTAS_SHIP
    &         ( am_I_Root, YEAR, Input_Opt, State_Chm, RC )
        ENDIF

At the end of the emissions subroutine calls for the full-chemistry simulation, make sure to reset FIRST to false.

        ! Reset first-time flag
        FIRST = .FALSE.

For consistency, this fix should also be applied to the specialty simulation code in DO_EMISSIONS.

--Melissa Sulprizio 14:19, 14 July 2014 (EDT)

Compilation error in ND63 diagnostic

This issue was resolved by the addition of the HEMCO emissions component into GEOS-Chem v10-01.

The following code has been removed from GEOS-Chem. HEMCO has now rendered the previous emissions routines obsolete.

Cenlin He wrote:

Recently, I have some problems compiling the latest version (v9-02) of GEOS-Chem. I downloaded the standard version of codes and did not change anything. When I compiled the code, it always showed as follows:
   ifort -cpp -w -O2 -auto -noalign -convert big_endian -vec-report0 -fp-model source 
   -openmp -mcmodel=medium -shared-intel -DLINUX_IFORT -DGEOS_5 -DGRID2x25 -I../Headers 
   -module ../mod -I/data/qiling/GEOS-Chem-Libraries/opt/ifort/nc4/include -c diag_mod.F

   fortcom: Error: diag_mod.F, line 257: This ALLOCATABLE attribute is invalid; 
   the ALLOCATABLE attribute can only be used when declaring array objects.   [AD63_COUNT] 
         INTEGER, ALLOCATABLE :: AD63_COUNT
   ------------------------------^

   fortcom: Error: diag_mod.F, line 471: An array-valued argument is required in this context.   [ALLOCATED]
     IF ( ALLOCATED( AD63_COUNT  ) ) DEALLOCATE( AD63_COUNT  )
   ----------------------^

   compilation aborted for diag_mod.F (code 1)
I checked GEOS-Chem wiki and did not find such reported problems. Then I searched in google and it might be because the compiler bug associated with the version of compilers. But I am not sure. Could you please give me some suggestions on how to solve this problem? Thanks in advance.

Bob Yantosca replied:

Thanks for writing. I think that is an error in the code that your compiler picked up. The AD63_COUNT variable is given the ALLOCATABLE attribute, but it is not an array.
The simple fix is to remove the ALLOCATABLE attribute from AD63_COUNT, so that the declaration reads:
    INTEGER :: AD63_COUNT
And then you can comment out the
    IF ( ALLOCATED( AD63_COUNT ) ) DEALLOCATE( AD63_COUNT )
statement as well. This should get you past the error.

--Bob Y. 15:55, 19 August 2014 (EDT)

Bug in tagged Hg emissions

This issue was resolved by the addition of the HEMCO emissions component into GEOS-Chem v10-01.

The following code has been removed from GEOS-Chem. HEMCO has now rendered the previous emissions routines obsolete.

Carey Friedman identified a bug that affects emissions of the Hg2 and HgP tagged tracers. For more information, please see this post on our Mercury wiki page.

--Melissa Sulprizio 16:44, 16 September 2014 (EDT)