Difference between revisions of "GEOS-Chem Newsletter Winter 2013"

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(New page: Dear GEOS-Chem users, We are happy to bring you the Winter 2013 edition of the GEOS-Chem Newsletter! Please read below to find out the latest goings-on in the GEOS-Chem community. Since...)
 
 
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:Dear colleagues and GEOS-Chem users:  
 
:Dear colleagues and GEOS-Chem users:  
  
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:Please take note of the January 31 registration deadline for the 6th International GEOS-Chem Meeting (IGC6) at Harvard University on May 6-9, 2013. Go to the meeting website [http://meeting.geos-chem.org meeting.geos-chem.org]] to register.  We expect the meeting to be oversubscribed.  You will hear of acceptance in mid-February.
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:Please take note of the '''January 31 registration deadline for the 6th International GEOS-Chem Meeting (IGC6)''' at Harvard University on May 6-9, 2013. Go to the meeting website [http://meeting.geos-chem.org '''''meeting.geos-chem.org'''''] to register.  We expect the meeting to be oversubscribed.  You will hear of acceptance in mid-February.
  
 
:Daniel Jacob<br>
 
:Daniel Jacob<br>
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GEOS-Chem Model Scientist  
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GEOS-Chem Model Scientist
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== GEOS-Chem Steering Committee ==
 
== GEOS-Chem Steering Committee ==
  
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=== Meetings ==
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=== GCSC Meetings ===
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The [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee] (GCSC) last met on '''Tuesday January 8th, 2013'''.  We invite you to read [http://acmg.seas.harvard.edu/geos/word_pdf_docs/steering_cmte/gc_sc_minutes_08Jan2013.pdf meeting minutes].
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The next GCSC telecon will take place in April 2012, date TBD.
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=== Elections ===
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== GEOS-Chem Support Team ==
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Here is a summary of [[GEOS-Chem Support Team]] activities:
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#Bob Yantosca has been working on the code to process GEOS-5.7.2 data (see below). He also oversees general GC development and the development of the Grid-Independent model.
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#Michael Long is primarily working on the Grid-Independent GEOS-Chem project (see below).
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#Melissa Payer has been working on general GC development tasks (i.e. code merging, generating 1-month benchmark simulations, user support, documentation, etc.).
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#Matt Cooper (Dalhousie) has been working on regridding the MERRA met data to 2&deg; x 2.5&deg; degree resolution (see below).  He has also begun replacing the existing regridding routines in GEOS-Chem with the MAP_A2A regridding package (which is what is currently use for regridding the GMAO met fields).
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== Public Release of v9-01-02 ==
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Since the previous GCSC telecon in November, the [[GEOS-Chem Support Team]] has issued a public release (on 28 Nov 2011) for GEOS-Chem v9-01-02.  Most of the updates in this version consisted of bug fixes and structural code changes.
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In addition to the bug fixes and structural changes, several several scientific updates were added to v9-01-02, namely:
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#[[Anthropogenic_emissions#Streets_2000|Imposed seasonality on David Streets NH3 emissions]] (Jenny Fisher, Harvard)
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#[[Dry deposition#Updated dry deposition velocities for aerosols over ice and snow|Updated dry deposition velocities for aerosols over ice and snow]] (Jenny Fisher, Harvard)
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#[[APM_aerosol_microphysics|APM Aerosol Microphysics Package]] (SUNY/Albany group)
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#[[Biomass_burning_emissions#GFED3|GFED3 biomass burning emissions]] (Prasad Kasibhatla, Duke)
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#[[Implementation of RETRO Anthropogenic Emissions]] (Wes Reinhart & Dylan Millet, UMN)
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#[[Mercury#Anthropogenic_Emissions|GEIA 2005 Hg emissions]] + updates for the Hg simulation (Team Hg)
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For detailed information about GEOS-5.7.2, please see the [[GEOS-Chem v9-01-02|GEOS-Chem v9-01-02 wiki page]].
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== GEOS-Chem v9-01-03 ==
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Here is a progress report on the development of [[GEOS-Chem v9-01-03]]:
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=== Updates that have been benchmarked ===
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As of this writing, the GEOS-Chem Support Team has added the following features to GEOS-Chem v9-01-03, and has validated each feature with the customary 1-month benchmark simulation.
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#[[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03a|v9-01-03a]]:
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#*[[Chemistry_Issues#GLCO3.2C_GLPAN_bug_in_standard_mechanism|Fix for GLCO3/GLPAN bug in standard chemistry mechanism]] (by Fabien Paulot).  This fixes a typo in the chemical mechanism input files which results in an artificial loss of NOx.
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#[[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03b|v9-01-03b]]:
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#*[[Acetone|Updated acetone ocean source & sink]] (by Emily Fischer).  This brings the acetone simulation more into line with current observations.
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#*[[Biogenic_emissions#Retirement_of_obsolete_GEIA_biogenic_emissions|Retirement of obsolete GEIA biogenic emissions]] (by Dylan Millet).  This removes obsolete legacy code, which will facilitate future G-C development.
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#[[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03c|v9-01-03c]]:
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#*[[Dry_deposition#OVOCs_dry_deposition|OVOC dry deposition]] (by Jingqiu Mao).  This update changes the reactivity factor for OVOC’s from 0 to 1 in the dry deposition code (cf. Karl et al, 2010)
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#[[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03d|v9-01-03d]]:
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#*[[Sea_salt_aerosols#SST_dependent_sea_salt_emissions|Improvements to sea salt emission]] (by Lyatt Jaegle).  Sea salt emissions now include a SST and wind speed dependency (cf. Jaegle et al 2011)
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#*[[Sea_salt_aerosols#Updates_to_sea_salt_dry_deposition|Improvements to dry deposition]] (by Lyatt Jaegle):
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#*#Use Zhang et al (2001) scheme for sea salt drydep over land
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#*#Use Slinn & Slinn (1980) scheme for sea salt drydep over oceans
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#*#Now use actual surface pressure in routine DEPVEL instead of a constant value (NOTE: this affects all species, not just sea salt)
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#*[[Mineral_dust_aerosols#Sub-micron_dust_mass_partitioning_change|Dust submicron size distribution for optics]] (by David Ridley, Colo State).  This update uses a more realistic partitioning of dust mass for photolysis.
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#[[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03e|v9-01-03e]]:
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#*[[Wet_deposition#Add_scavenging_by_snow|Add scavenging by snow]] (by Qiaoqiao Wang).  This update only lets dust, hydrophobic BC, and HNO3 be “rained out” by snow.
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#*[[Wet_deposition#Updates_for_aerosol_scavenging_efficiency|Updates for aerosol scavenging efficiency]] (by Qiaoqiao Wang).  This follows the scheme of Feng (2007, 2009) to avoid over-scavenging of aerosols.
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#*NOTE: A [[GEOS-Chem_v9-01-03_benchmark_history#Rn-Pb-Be_simulation|1-year Rn-Pb-Be benchmark simulation]] was performed in addition to the customary 1-month fullchem benchmark.
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=== Updates slated for inclusion ===
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The following updates are currently slated for inclusion into v9-01-03 (order subject to change):
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#[[Ship_emissions#PARANOX_ship_plume_model|PARANOX ship plume emissions model]] (Geert Vinken, Eindhoven)
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#Updates from the [[Grid-independent_GEOS-Chem]] (Mike Long, Harvard)
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#[[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|SOA simulation with semi-volatile POA]] (Havala Pye, EPA + GCST)
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#[[Stratospheric_chemistry|Stratopsheric monthly climatological P and k]] (Lee Murray, Harvard)
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#Various emissions updates, including:
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#*[[EPA/NEI05_North_American_emissions|EPA/NEI05 North American Hg emissions]]
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#*Streets future Hg emissions
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#*Satellite-based NOx emission trends
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#*[[Sources_and_Sinks_Working_Group#Available_Historical_and_Future_Emissions|Historical emission inventories of SO2, NOx, BC, and POA]]
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#*Daily and hourly GFED3 biomass emissions
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#*Add scaling of lightning NOx for 2x2.5 MERRA simulations
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#Nested grid simulation updates:
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#*[[Mercury#Nested-grid_Hg_simulation_over_North_America|Nested-grid Hg simulation]]
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#*[[CO2_simulation#Nested-grid_CO2_simulation|Nested-grid CO2]]
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#Offine simulation updates:
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#*[[Tagged_Ox_simulation#Replace_LD65_with_LLTROP_in_tagged_ox_mod.F|Updated tagged Ox simulation]] – mostly to correct inconsistencies in the existing source code (Dylan Jones, Toronto & Hongyu Liu, NIA)
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#*[[CH4_simulation#Update_methane_emissions_and_add_capability_for_North_America_nested_grid|Updated offline CH4 simulation]] (Kevin Wecht, Harvard)
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#Various minor bug fixes, including:
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#*[[Nested_Model_Working_Group#Fixes_to_Streets_emissions_for_model_years_2005_and_earlier|Bug fixes for David Streets emissions for years 2005 and earlier]] (Jenny Fisher, Harvard)
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#*[[Nested_Model_Working_Group#Fixes_to_Streets_emissions_for_model_years_2005_and_earlier|Bug fix in emep_mod.F for offline simulations]] (GCST)
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#*[[GEOS-Chem_v9-01-02#Fixes_in_emep_mod.f|Bug fix to prevent crash in wetdep when encountering bad met input]] (GCST)
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#*[[Wet_deposition#Anomalous_PRECTOT_values_on_22_July_2010|Minor fix in Rn-Pb-Be simulation to prevent missing drydep diagnostics]] (GSCT)
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#*[[GEOS-Chem_v9-01-03#Bug_fixes_in_diag3.F|Bug fixes in diag3.F]] (Mat Evans, York)
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#*[[GEOS-Chem_v9-01-03#Bug_fixes_for_nested-grid_simulation|Bug fixes for nested-grid simulation]] (Dylan Millet, UMN)
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#*[[CH4_simulation#Error_reading_GWETTOP_fields|Bug fix for reading GWETTOP fields in offline CH4 simulation]] (GCST)
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#*[[GEOS-Chem_v9-01-03#Correct_out-of-bounds_error_in_offline_aerosol_simulation|Correct out-of-bounds error in offline aerosol simulation]] (GCST)
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#[[Development_of_Fast-JX_in_GEOS-Chem|Updating photolysis from FAST-J to FAST-JX]]
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The GEOS-Chem Support Team shall lump together updates that do not affect the full chemistry simulation for expediency in benchmarking.
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Also, the GEOS-Chem Support Team recommends that updates from the [[Grid-independent GEOS-Chem]] be merged into the standard repository as soon as possible (ideally before the SOA + POA updates).  This will prevent the Grid-independent GEOS-Chem code from significantly diverging from the standard mainline GEOS-Chem code.  In the future, further synchronization between the Grid-Independent GEOS-Chem and the standard GEOS-Chem will be necessary at frequent intervals.
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== Grid-Independent GEOS-Chem ==
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Since the previous GEOS-Chem Steering Committee telecon in November 2011, work on the [[Grid-independent GEOS-Chem]] (GIGC) has progressed swiftly.  Among the milestones:
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#Old Fortran-77 style legacy code has been replaced with modern Fortran-90 code. 
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#Common blocks have been replaced by Fortran modules.
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#The IIPAR and JJPAR parameters are now defined at runtime rather than being left as fixed parameters.  This will allow a larger model to be able to tell the GIGC code the size of the grid rather than having to use a hardwired grid.
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#Fortran-90 derived-type arrays have been created for both emissions tendencies and met fields.  At present, these point to the existing emissions and met field variables in the code.  In the future, these new derived type arrays will replace the existing arrays.
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Mike Long summarizes:
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The [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee] (GCSC) last met on '''Tuesday January 8th, 2013'''.  We invite you to read [http://acmg.seas.harvard.edu/geos/word_pdf_docs/steering_cmte/gc_sc_minutes_08Jan2013.pdf the meeting minutes].
  
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<blockquote>
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The next GCSC telecon will take place on '''Friday, April 12, 2013 at 10:00 AM ET (14:00 GMT)'''.  If you have any items for the Steering Committee, then please bring them to the attention of your [http://acmg.seas.harvard.edu/geos/geos_working_group Working Group chairpersons].
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<p>After a few false-starts, the system is now capable of operating on a flexible grid, primarily due to flexing F90 strengths in place of F77.  I am right now in the process of validating that the model results are still good & I haven't broken anything.  But, it has not yet been tested with ESMF. That will be next.</p>
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<p>The data streams have been largely reconfigured in preparation for ESMF coupling through simple-bundle sockets, and that will be the largest next-step prior to running the 'sandbox' as Bob Yantosca and Arlindo da Silva had set up previously.</p>
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<p>Also, it is noteworthy that this development has been in stride with GEOS-Chem science development and updates; and new features and fixes are being brought into this system as they are brought into the standard code.”</p>
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</blockquote>
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As of this writing, Mike Long is visiting the Beijing Climate Data Center.  He is working with the staff there to insert the Grid-Independent GEOS-Chem code into the Center’s GCM.  This will help to further refine the GIGC source code.
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=== GCSC Elections ===
  
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Mike writes from Beijing:
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'''''[mailto:djacob@fas.harvard.edu Daniel Jacob] wrote:'''''
  
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<blockquote>
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:Dear GEOS-Chem user:
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<p>“We're making progress. We're effectively reading some of the emissions files onto the GCM.</p>
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<p>DO_CHEMISTRY (i.e. GEOS-Chem’s chemistry driver routine) is working in [the Bejing Climate Data Center’s MPI-parallel version of the CAM GCM] on an externally initialized decomposed grid w/o blowing up.  Note, that there aren't any 'true' data links between CAM & GC other than the geophysical grid and the the model’s time & time-stepping states.  [T]he system isn't dying.</p>
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<p>What’s left to do:</p>
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#Getting CAM to read GC's land-type, dry depositon, and other ASCII input files regardless of the grid.  We may settle for a blunt-force regridding operation for the time being.  
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:A number of [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Working Group Co-Chair] positions on the GEOS-Chem Steering Committee (GCSC) will become available as terms end in May.  New co-chairs will be elected at the [http://meeting.geos-chem.org 6th International GEOS-Chem Meeting].  Please let me know if you are interested in serving.  Click [http://acmg.seas.harvard.edu/geos/word_pdf_docs/steering_cmte/gcsc_functioning.pdf HERE] to learn more about the functions and responsibilities of the GCSC and about the different WGs. We eagerly encourage qualified candidates to apply. We are particularly interested in maintaining the international character of the GCSC.
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#Complete a proper emissions read & build-up. My approach is simply going to have CAM read in all the data from file, and then modify the DO_EMISSIONS routine (i.e. GEOS-Chem’s emissions driver routine) to [accept the data input].”
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</blockquote>
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Upon Mike’s return from Beijing, we shall ingest the GIGC source code into the standard GEOS-Chem repository.  This step is critical to ensure that the GIGC code does not diverge significantly from the mainline GEOS-Chem code.
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:Daniel Jacob<br>GEOS-Chem Model Scientist<br>for the GCSC
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<p>Work remaining to be done:</p>
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#Further debugging
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== GEOS-Chem v9-01-03 was released in September 2012 ==
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#Wrapping the GIGC code with calls to the Earth System Model Framework library.
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#Separating the emissions routines from the rest of the code
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#Converting file I/O from binary to netCDF
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#Integrating GIGC code within NASA/GMAO’s GEOS-5 GCM
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== GEOS-5.7.2 met field update ==
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The current released version of GEOS-Chem is [[GEOS-Chem v9-01-03|v9-01-03]], released in September 2012. If you have not updated to this version, we encourage you to do so at your earliest convenience.
  
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This past summer, NASA/GMAO updated the operational GEOS system from GEOS-5.2.0 to [[GEOS-5.7.2]].  Here is a quick summary of the new GEOS-5.7.2 data product:
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For a complete list of all new features and fixes in GEOS-Chem v9-01-03, [[GEOS-Chem_v9-01-03#What.27s_new_in_this_version|please see this table]].  We also invite you to view the [http://acmg.seas.harvard.edu/geos/doc/archive/man.v9-01-03/index.html Online GEOS-Chem User's Manual] for more information.
  
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#Horizontal resolution: 0.25&deg; lat x 0.3125&deg; lon (i.e. 1/4&deg; x 5/16&deg;)
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Starting with v9-01-03, users must have a netCDF library installation on their systems in order to run GEOS-Chem. To simplify the library installation process, we have created the <tt>GEOS-Chem-Libraries</tt> installer package. Detailed instructions about how to download and install netCDF with <tt>GEOS-Chem-Libraries</tt> may be found on our [[Installing libraries for GEOS-Chem]] wiki page.
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#Vertical resolution: 72 hybrid layers (identical to the vertical grids used by the GEOS-5.2.0 and MERRA met data products)
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#[[GEOS-5.7.2#GEOS-5.7.2_time_archiving|Time resolution]]: Hourly and 3-hourly data (timestamps very similar to MERRA)
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#Input data format: netCDF-4 (as opposed to HDF4-EOS, used for past GMAO data products)
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Bob Yantosca has been preparing GEOS-Chem to run with the new GEOS-5.7.2 met data.  He has completed the following tasks:
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== GEOS-Chem v9-02 news ==
  
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#Added documentation to the GC wiki with information about the GEOS-5.7.2 data.
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=== Development ===
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#Activated a “data subscription” for the GEOS-5.7.2 data.
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#Written scripts to transfer GEOS-5.7.2 data from NASA to Harvard and to automate the data download process.
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#Finalized the GEOS-5.7.2 data processing/regridding software.
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#Created a new Git repository for GEOS-5.7.2 data processing code and scripts.
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#Completed initial modifications in GEOS-Chem to read the GEOS-5.7.2 data.
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For more information about the implementation of GEOS-5.7.2 into GEOS-Chem (including a detailed list of all modifications made to individual GEOS-Chem routines), please see the following wiki pages:
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As of this writing (09 Jan 2013), we have completed the following benchmarks for [[GEOS-Chem v9-02]]:
  
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#[[GEOS-5.7.2]]
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We have completed the following benchmarks:
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#[[List of GEOS-5.7.2 met fields]]
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#[[GEOS-5.7.2 implementation details]]
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We plan to store the GEOS-5.7.2 following data at Harvard (which will be downloadable by the community).  Data will be processed for Aug 2011-onward.  Priority will be given to these grids:
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#[[GEOS-Chem_v9-02_benchmark_history#v9-02a|v9-02a]]: Correction for PBL heights
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#[[GEOS-Chem_v9-02_benchmark_history#v9-02b|v9-02b]]: New soil NOx emissions module + minor bug fixes
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#[[GEOS-Chem_v9-02_benchmark_history#v9-02c|v9-02c]]: Updates for the Hg simulaton: emissions + kinetics
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#[[GEOS-Chem_v9-02_benchmark_history#v9-02d|v9-02d]]: Structural updates for the Grid-Independent GEOS-Chem
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#[[GEOS-Chem_v9-02_benchmark_history#v9-02e|v9-02e]]: Bug fix for regridding of anthro emissions (Streets, NEI2005)
  
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#Global 2&deg; x 2.5&deg;
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We are still working on the following benchmarks:
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#Global 4&deg; x 5&deg;
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#SEA4CRS Nested grid 0.25&deg; x 0.3125&deg;: 20S-50N; 60E-150E
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Consistent with our [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf established nested grid protocol], we will distribute the GEOS-5.7.2 data processing code & scripts to any user groups who wish to pull the nested data themselves.
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#The [[Hg and POPs Working Group]] is working on a 1-yr [[Mercury|Hg simulation]], based on v9-02c.
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#The [[Nested Model Working Group]] is performing a 1-yr [[NOx-Ox-HC-aerosol|full-chemistry simulation]] for the North American Nested Grid with GEOS-5 met (0.5&deg; x 0.666&deg;).  They have completed 6 months of the benchmark.
  
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One important new feature is that the GEOS-Chem Support Team shall be archiving the processed GEOS-5.7.2 data in [[#Transition to netCDF file format| netCDF format]] instead of the traditional binary format (see below for more information).
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The next set of updates to [[GEOS-Chem v9-02]] shall be chemistry updates, including:
  
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At present, GEOS-Chem can read the GEOS-5.7.2 met data from within the timestepping loop in the main program for 2&deg; x 2.5&deg;, 4&deg; x 5&deg; global grids and the 0.25&deg; x 0.3125&deg; SEA4CRS nested China grid.  Further testing is required to make sure that the individual operations (i.e. convection, deposition, chemistry) will work properly with the GEOS-5.7.2 data.
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#Updating rate constants for consistency with observations
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#[[ChemTelecon20111202|Update to isoprene scheme]]
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#[[ChemTelecon20111202|Include HO2 uptake onto aerosol]]
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#Putting inhibition to N2O5 uptake.  
  
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Bob Yantosca and the SEA4CRS team (Jenny Fisher, Patrick Kim, Lin Zhang, Yuxuan Wang) are coordinating several of the remaining tasks (e.g. regridding emissions data files, debugging, etc.) among themselves.
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We shall run 1-month and 1-year benchmarks at intermediate points the development in order to better assess how these updates impact the simulation results.
  
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== MERRA met field update ==
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=== Bugs and fixes ===
  
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Matt Cooper has been regridding the GMAO MERRA data to 2&deg; x 2.5&deg; resolution at Dalhousie.  He will continue the data processing until the full record is completed.  He writes:
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[[GEOS-Chem v9-02]] shall contain fixes for the following bugs and/or technical issues:
  
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<blockquote>As for MERRA 2x2.5, I have finished processing the whole data record, and we have 1979-2010 available on our server here at Dal. I've already updated the wiki to indicate that, and have been contacted by a few people already. Feel free to spread the word that we have these met fields available.</blockquote>
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#[[Boundary_layer_mixing#Updates_on_GEOS-5_PBL_height_.26_diurnal_variation_of_aerosols|Correction for GEOS-5 PBL heights]]
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#[[Tagged_CO_simulation#Bug_fixes_for_tagged_CO_simulation|Bug fixes for tagged CO simulation]]
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#[[EPA/NEI05_North_American_emissions#Bug_fix_in_nei2005_anthro_mod.F|Regridding error in NEI2005 emissions]]
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#[[GEOS-Chem v9-02#Bug fix for updated CAC emissions|Bug fix for updated CAC emissions]]
 +
#[[Bromine_chemistry_mechanism#Bug_fix_for_Br2_emissions|Fixed incorrect loop limits in Br2 emissions code]]
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#[[GEOS-Chem v9-02#Bug fixes in biofuel_mod.F and emfossil.F|Bugs in diurnal NOx scaling and biofuel double-counting]]
  
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== Transition to netCDF file format ==
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=== Other updates ===  
  
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Several GEOS-Chem users have identified a clear need to migrate GEOS-Chem from the traditional sequential binary file format (aka “binary punch” or “bpch”) to netCDF format.  NetCDF is a self-describing file format that allows one to save the data along with any descriptions of the data (field names, units, descriptions.  Several software packages for data visualization and analysis support netCDF format.
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Please see [[GEOS-Chem v9-02#What's new in this version|this table]] for the complete list of updates that shall be added to GEOS-Chem v9-02.  We also invite you to view the list of [[GEOS-Chem model development priorities]], as determined by [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html Steering Committee], with input from the [http://acmg.seas.harvard.edu/geos/geos_working_groups.html Working Groups].
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The GEOS-Chem Support Team recommends migration to netCDF format in order to facilitate the Grid-Independent GEOS-Chem (GIGC) project.  As described above, the GIGC seeks to incorporate GEOS-Chem within larger Earth System Models, Climate Models, GCMs, and data assimilation systems. These larger models employ Message Passing Interface (MPI) parallelization in order distribute or “decompose” data among several hundreds or thousands of CPUs.
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The current “binary punch” format used by GEOS-Chem is incompatible with MPI parallelization in the sense that small chunks of a binary punch file cannot be read simultaneously across CPUs in a distributed memory environment.  Rather, the entire file must be read on each CPU that is executing, thus adding much more file I/O overhead to the system, which in turn negatively impacts model performance and scalability.  On the other hand, it is possible to read small chunks from a netCDF file independently on several CPUs simultaneously, thus preserving scalability.
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== Grid-Independent GEOS-Chem news ==
  
−
The transition to netCDF file format will involve several steps.  We realize that the full transition cannot be achieved overnight.  The first step shall be to modify GEOS-Chem to be able to read netCDF data files from disk, starting with the new [[GEOS-5.7.2]] met data product.  To this end, Bob Yantosca has installed his NcdfUtilities package into a development version of GEOS-Chem v9-01-03.  Bob has also written a Fortran module (“geos57_read_mod.F90”) which calls NcdfUtilities routines to read the GEOS-5.7.2 met data from disk.  The netCDF functionality can be activated simply by compiling GEOS-Chem code with an additional switch (NETCDF=yes).
+
Much of the recent [[Grid-independent GEOS-Chem]] (aka GIGC) work has involved restructuring how data flows between routines in the standard GEOS-Chem code. In general, we now make use of derived-type objects to carry data fields instead of referencing arrays from other modules with USE statements.  We have been making these types of structural updates concurrently with scientific development in GEOS-Chem in order to avoid the GIGC code from lagging behind the standard GEOS-Chem code.
  
−
At a later time, in conjunction with the GIGC project, we shall also begin to convert GEOS-Chem’s diagnostic outputs to netCDF format.  Fortran code for writing netCDF files is necessarily much more “wordy“ than code for reading from netCDF files because one must supply information (aka “metadata”) about the variables that will constitute each netCDF file.  To simplify the coding process for the GEOS-Chem community, Bob Yantosca has included into GEOS-Chem some Perl scripts which will automatically generate the proper Fortran for both writing to and reading from netCDF files.
+
We’ve also streamlined the [http://www.earthsystemmodeling Earth System Model Framework (ESMF)] interface that connects GEOS-Chem to the GEOS-5 GCM.  The ESMF interface can now deliver the following information from the GCM to GEOS-Chem:
  
−
The Earth System Model Framework environment contains many file I/O and regridding utilities.  Once the GIGC code becomes fully compatible with ESMF, we will take advantage of ESMF’s regridding capabilities.  During construction of the GIGC, we will need to continue to provide a Fortran-only package for netCDF I/O (cf. Bob Yantosca’s NcdfUtilities, or similar programs).
+
#Size of data arrays on each CPU: (<tt>IIPAR</tt>, <tt>JJPAR</tt>, <tt>LLPAR</tt>)
 +
#Size of the entire global grid: (<tt>IM_WORLD</tt>, <tt>JM_WORLD</tt>, <tt>LM_WORLD</tt>)
 +
#Corner grid box indices on each CPU (<tt>I_LO</tt>, <tt>I_HI</tt>, <tt>J_LO</tt>, <tt>J_HI</tt>)
 +
#Date and time from the GCM
 +
#Level edge pressures from the GCM
  
−
The migration to netCDF will require that GEOS-Chem end users install the netCDF libraries on their system.  We shall provide [[Installing_HDF5_and_netCDF4|instructions for installing these libraries]] on the GEOS-Chem wiki.
+
We also made sure to bring the ESMF interface up-to-date with the tracers and species introduced by the latest [[Bromine chemistry mechanism|bromine chemistry mechanism]].
  
−
The next release of the GAMAP visualization software (v2-16) will feature improved support for reading and plotting data in netCDF files.  The GAMAP routines BPCH2COARDS and MAKE_MULTI_NC may be used to convert existing binary punch files to netCDF format.
+
All of these updates are now reflected on the GIGC wiki pages.  Please see:
  
−
== De-supporting of GEOS-3 meteorology ==
+
#[[Grid-Independent GEOS-Chem]]
 +
#[[Grid-Independent GEOS-Chem: Chemistry Component]]
 +
#[[HEMCO|Grid-Independent GEOS-Chem: Emissions Component]]
 +
#[[Derived type objects used by GEOS-Chem|Derived type objects used by the Grid-Independent GEOS-Chem]]
 +
#[[Programming techniques for HPC environments|Programming techniques used for the Grid-Independent GEOS-Chem]]
  
−
The [[Overview_of_GMAO_met_data_products#GEOS-3|GMAO GEOS-3 met data product]] is now several versions behind the current GMAO operational product ([[GEOS-5.7.2]]).  The GEOS-3 data period only covered the years 2000-2002 (with some data in 1998).   
+
We recently performed a test simulation of GEOS-Chem in our ESMF “Sandbox” environment, which replicates the connection to the GEOS-5 GCM without having to run the full GCM.  We demonstrated that GEOS-Chem could be successfully run within the ESMF environment using MPI parallelization.   
  
−
Bob Yantosca queried the GEOS-Chem user community to see if there were any users who still relied on the GEOS-3 met data for their research.  He found that none of the GEOS-Chem users still rely on GEOS-3 meteorology.
+
Christoph Keller is working on the [[HEMCO|GIGC Emissions Component]], which will run independently of the chemistry.  The Emissions Component will combine emissions from several inventories, apply the relevant scale factors, regrid the emissions, and pass them to the GIGC Chemistry Component via the ESMF interface.  Christoph has been making use of a new data structure to store emissions.  He is also handling disk I/O operations separately from the data structure, which is a requirement of the ESMF environment.  Please see [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/ckeller_emissions_group_mtg_20121218_web.pdf this presentation] for further details.
  
−
Therefore, the GEOS-Chem Support Team recommends that we remove support for GEOS-3 met data from within GEOS-Chem.  This will help to clean up the GEOS-Chem source code and remove unnecessary routines and coding constructs which may impede development of the [[Grid-independent GEOS-Chem]].
+
Still to do:
  
−
== Other development tasks ==
+
#Modify the GIGC code to read data from ASCII input files (i.e. <tt>input.geos</tt>, <tt>globchem.dat</tt>, <tt>ratj.d</tt>, etc.) on the root CPU, and to broadcast the data to other CPUs.  This is necessary in order to prevent all CPUs on the system from performing disk I/O operations simultaneously.
 +
#Bring [[Dry deposition|dry deposition]] into the ESMF interface.  Mike Long has been working on this.
 +
#Port the updated GEOS-Chem source code back to NASA/GSFC to allow testing of the GEOS-5/GEOS-Chem combined model on NASA machines.
  
−
Matt Cooper has been working on replacing the traditional GEOS-Chem regridding routines (which sometimes involve two separate regrdidding processes) with the MAP_A2A regridding package.  He writes:
+
We anticipate to be able to run a GEOS-5 GCM/GEOS-Chem simulation before the [http://meeting.geos-chem.org IGC6 meeting in May].  Stay tuned for results!
  
−
<blockquote>I'm making progress on getting MAP_A2A into GEOS-Chem. I have made the switch in some places and now am just working my way through the code finding all the places where it needs to be switched. Hopefully it doesn't take me too much longer.</blockquote>
+
== GEOS-Chem Adjoint News ==
  
−
== Downtime at Harvard: Feb 19-23, 2012 ==
+
[[GEOS-Chem Adjoint v34]] is now the standard version of the GEOS-Chem adjoint model.  Please see [[GEOS-Chem_Adjoint_v34#What.27s_new_in_this_version|this table]] for a list of new features in v34.
  
−
The Harvard Atmospheric Chemistry Modeling Group will be moving its computational resources from its existing location into a more modern server room.  The transition will take place starting on Sunday Feb 19, 2012 and will take at 3-4 days to complete.
+
Some key improvements:
  
−
Our sysadmin Jack Yatteau writes:
+
#The adjoint code is now distributed using Git instead of CVS.  Users of the adjoint model will need to re-register in order to download the adjoint source code from the new Git repository:
 +
#Makefiles were updated to better follow the makefile structure used by the forward model.  For more information please see [http://adjoint.colorado.edu/~yanko/gcadj_std/GC_adj_man.pdf this link].
 +
#Implemented GFED3 emissions.
  
−
Downtime:
+
Most of the additions to v34 were technical software updates.  The next version of the GEOS-Chem adjoint will have more scientific updates.
−
        1) Sunday, February 19, 16:00. Most services will go down.
+
−
        Running jobs on the computational cluster will be rescheduled.
+
−
        Minimal services will remain up overnight and go down early Monday
+
−
        morning.  Some services might be available Tuesday.  Interactive
+
−
        and batch systems should be available by EOB Wednesday 2/22.
+
−
+
−
        2) Thursday, February 23.  Backup power for our equipment
+
−
        will be unavailable for a few hours due to UPS maintenance.
+
−
        No downtime is anticipated, but we will not be protected against
+
−
        power failure while the work is being performed.
+
  
−
The following services will be unavailable during the transition:
+
Please contact GEOS-Chem Support Team Adjoint Specialist [mailto:mailto:boun0479@gmail.com Nicolas Bousserez] for specific support requests regarding the GEOS-Chem Adjoint code.
  
−
#<tt>ftp.as.harvard.edu</tt>: main FTP site for data downloads
+
== In other news ==
−
#<tt>git.as.harvard.edu</tt>: Git server for GEOS-Chem source code & run directory downloads
+
−
#[http://acmg.seas.harvard.edu/ GEOS-Chem web site]
+
−
#[http://acmg.seas.harvard.edu/ GAMAP web site]
+
−
#[http://acmg.seas.harvard.edu/ Jacob Group web site]
+
  
−
The GEOS-Chem wiki is hosted on a different server and should not be affected.  However, some links to documents on the GEOS-Chem web server will not function during the downtime.
+
Here are some other noteworthy news items ...
  
−
Please plan accordingly.  Met data may also be obtained from the Dalhousie server (<tt>rain.ucis.dal.ca</tt>)
+
#<p>The [[GEOS-Chem Support Team|GEOS-Chem Support Team (GCST)]] is currently investigating why [[NOx-Ox-HC-aerosol|full-chemistry simulations]] done with [[GEOS-Chem v9-01-03]] and [[GEOS-Chem v9-02]] take longer to run than older model versions.  Melissa Payer is taking the lead on this effort.</p>
 +
#<p>We are continuing to work on the 0.25&deg; x 0.3125&deg; nested grid capability with the GEOS-5 “FP” (formerly known as [[GEOS-5.7.2]]) met fields.  Sajeev Philip (GCST member, Dalhousie) will be extracting and regridding the met data.  We are preparing to have this high-resolution nested grid capability ready for the revamped SEAC4RS mission this fall.  The GCST is collaborating with Yuxuan Wang (Tsinghua), Jenny Fisher (Wollongong), Lin Zhang (Peking U.), Patrick Kim (Harvard) and others towards this end.</p>
 +
#<p>Jeff Pierce (CSU) recently hired programmer Sal Farina to synchronize the [[TOMAS aerosol microphysics]] package with the latest GEOS-Chem code.  TOMAS had been integrated into [[GEOS-Chem v8-03-01]], but further TOMAS development lagged behind the standard GEOS-Chem.</p>
 +
#<p>Sebastian Eastham (working w/ Steven Barrett @ MIT) has deliverd a new aircraft emissions module (AEIC) to the GCST.  This new aircraft emissions package is slated to be added into [[GEOS-Chem v9-02]], along with other emissions updates.</p>
 +
#<p>Prasad Kasibhatla (Duke) has prepared GFED3 emissions throughout the end of 2011 (the previous data ended in 2010).  The new data are stored on the Harvard server.  We plan to standardize support for the extended GFED3 data as part of our "emissions update" to [[GEOS-Chem v9-02]].</p>
 +
#<p>Debra Weisenstein (Harvard) and Steven Barrett (MIT) are working on a state-of-the-art OCS simulation for GEOS-Chem.</p>
 +
#<p>Colette Heald (MIT) is working with AER Corp. to install the RRTMG radiative transfer model into GEOS-Chem.</p>
 +
#<p>We invite you to view the [https://trello.com/board/geos-chem-support-team/4fe36668fc79a1d3540ba80b GEOS-Chem board on Trello.com] to see the current tasks that we are working on now.  We update this board whenever we complete tasks (cards are archived for future reference).</p>
  
−
--[[User:Bmy|Bob Y.]] 11:21, 14 February 2012 (EST)
+
--[[User:Bmy|Bob Y.]] 14:57, 9 January 2013 (EST)

Latest revision as of 14:08, 19 June 2019

Dear GEOS-Chem users,

We are happy to bring you the Winter 2013 edition of the GEOS-Chem Newsletter! Please read below to find out the latest goings-on in the GEOS-Chem community.

Sincerely,

The GEOS-Chem Support Team
geos-chem-support@as.harvard.edu

Last call to register for the 6th International GEOS-Chem Meeting!

Daniel Jacob wrote:

Dear colleagues and GEOS-Chem users:
Please take note of the January 31 registration deadline for the 6th International GEOS-Chem Meeting (IGC6) at Harvard University on May 6-9, 2013. Go to the meeting website meeting.geos-chem.org to register. We expect the meeting to be oversubscribed. You will hear of acceptance in mid-February.
Daniel Jacob

GEOS-Chem Model Scientist

GEOS-Chem Steering Committee

GCSC Meetings

The GEOS-Chem Steering Committee (GCSC) last met on Tuesday January 8th, 2013. We invite you to read the meeting minutes.

The next GCSC telecon will take place on Friday, April 12, 2013 at 10:00 AM ET (14:00 GMT). If you have any items for the Steering Committee, then please bring them to the attention of your Working Group chairpersons.

GCSC Elections

Daniel Jacob wrote:

Dear GEOS-Chem user:
A number of GEOS-Chem Working Group Co-Chair positions on the GEOS-Chem Steering Committee (GCSC) will become available as terms end in May. New co-chairs will be elected at the 6th International GEOS-Chem Meeting. Please let me know if you are interested in serving. Click HERE to learn more about the functions and responsibilities of the GCSC and about the different WGs. We eagerly encourage qualified candidates to apply. We are particularly interested in maintaining the international character of the GCSC.
Daniel Jacob
GEOS-Chem Model Scientist
for the GCSC

GEOS-Chem v9-01-03 was released in September 2012

The current released version of GEOS-Chem is v9-01-03, released in September 2012. If you have not updated to this version, we encourage you to do so at your earliest convenience.

For a complete list of all new features and fixes in GEOS-Chem v9-01-03, please see this table. We also invite you to view the Online GEOS-Chem User's Manual for more information.

Starting with v9-01-03, users must have a netCDF library installation on their systems in order to run GEOS-Chem. To simplify the library installation process, we have created the GEOS-Chem-Libraries installer package. Detailed instructions about how to download and install netCDF with GEOS-Chem-Libraries may be found on our Installing libraries for GEOS-Chem wiki page.

GEOS-Chem v9-02 news

Development

As of this writing (09 Jan 2013), we have completed the following benchmarks for GEOS-Chem v9-02:

We have completed the following benchmarks:

  1. v9-02a: Correction for PBL heights
  2. v9-02b: New soil NOx emissions module + minor bug fixes
  3. v9-02c: Updates for the Hg simulaton: emissions + kinetics
  4. v9-02d: Structural updates for the Grid-Independent GEOS-Chem
  5. v9-02e: Bug fix for regridding of anthro emissions (Streets, NEI2005)

We are still working on the following benchmarks:

  1. The Hg and POPs Working Group is working on a 1-yr Hg simulation, based on v9-02c.
  2. The Nested Model Working Group is performing a 1-yr full-chemistry simulation for the North American Nested Grid with GEOS-5 met (0.5° x 0.666°). They have completed 6 months of the benchmark.

The next set of updates to GEOS-Chem v9-02 shall be chemistry updates, including:

  1. Updating rate constants for consistency with observations
  2. Update to isoprene scheme
  3. Include HO2 uptake onto aerosol
  4. Putting inhibition to N2O5 uptake.

We shall run 1-month and 1-year benchmarks at intermediate points the development in order to better assess how these updates impact the simulation results.

Bugs and fixes

GEOS-Chem v9-02 shall contain fixes for the following bugs and/or technical issues:

  1. Correction for GEOS-5 PBL heights
  2. Bug fixes for tagged CO simulation
  3. Regridding error in NEI2005 emissions
  4. Bug fix for updated CAC emissions
  5. Fixed incorrect loop limits in Br2 emissions code
  6. Bugs in diurnal NOx scaling and biofuel double-counting

Other updates

Please see this table for the complete list of updates that shall be added to GEOS-Chem v9-02. We also invite you to view the list of GEOS-Chem model development priorities, as determined by Steering Committee, with input from the Working Groups.

Grid-Independent GEOS-Chem news

Much of the recent Grid-independent GEOS-Chem (aka GIGC) work has involved restructuring how data flows between routines in the standard GEOS-Chem code. In general, we now make use of derived-type objects to carry data fields instead of referencing arrays from other modules with USE statements. We have been making these types of structural updates concurrently with scientific development in GEOS-Chem in order to avoid the GIGC code from lagging behind the standard GEOS-Chem code.

We’ve also streamlined the Earth System Model Framework (ESMF) interface that connects GEOS-Chem to the GEOS-5 GCM. The ESMF interface can now deliver the following information from the GCM to GEOS-Chem:

  1. Size of data arrays on each CPU: (IIPAR, JJPAR, LLPAR)
  2. Size of the entire global grid: (IM_WORLD, JM_WORLD, LM_WORLD)
  3. Corner grid box indices on each CPU (I_LO, I_HI, J_LO, J_HI)
  4. Date and time from the GCM
  5. Level edge pressures from the GCM

We also made sure to bring the ESMF interface up-to-date with the tracers and species introduced by the latest bromine chemistry mechanism.

All of these updates are now reflected on the GIGC wiki pages. Please see:

  1. Grid-Independent GEOS-Chem
  2. Grid-Independent GEOS-Chem: Chemistry Component
  3. Grid-Independent GEOS-Chem: Emissions Component
  4. Derived type objects used by the Grid-Independent GEOS-Chem
  5. Programming techniques used for the Grid-Independent GEOS-Chem

We recently performed a test simulation of GEOS-Chem in our ESMF “Sandbox” environment, which replicates the connection to the GEOS-5 GCM without having to run the full GCM. We demonstrated that GEOS-Chem could be successfully run within the ESMF environment using MPI parallelization.

Christoph Keller is working on the GIGC Emissions Component, which will run independently of the chemistry. The Emissions Component will combine emissions from several inventories, apply the relevant scale factors, regrid the emissions, and pass them to the GIGC Chemistry Component via the ESMF interface. Christoph has been making use of a new data structure to store emissions. He is also handling disk I/O operations separately from the data structure, which is a requirement of the ESMF environment. Please see this presentation for further details.

Still to do:

  1. Modify the GIGC code to read data from ASCII input files (i.e. input.geos, globchem.dat, ratj.d, etc.) on the root CPU, and to broadcast the data to other CPUs. This is necessary in order to prevent all CPUs on the system from performing disk I/O operations simultaneously.
  2. Bring dry deposition into the ESMF interface. Mike Long has been working on this.
  3. Port the updated GEOS-Chem source code back to NASA/GSFC to allow testing of the GEOS-5/GEOS-Chem combined model on NASA machines.

We anticipate to be able to run a GEOS-5 GCM/GEOS-Chem simulation before the IGC6 meeting in May. Stay tuned for results!

GEOS-Chem Adjoint News

GEOS-Chem Adjoint v34 is now the standard version of the GEOS-Chem adjoint model. Please see this table for a list of new features in v34.

Some key improvements:

  1. The adjoint code is now distributed using Git instead of CVS. Users of the adjoint model will need to re-register in order to download the adjoint source code from the new Git repository:
  2. Makefiles were updated to better follow the makefile structure used by the forward model. For more information please see this link.
  3. Implemented GFED3 emissions.

Most of the additions to v34 were technical software updates. The next version of the GEOS-Chem adjoint will have more scientific updates.

Please contact GEOS-Chem Support Team Adjoint Specialist Nicolas Bousserez for specific support requests regarding the GEOS-Chem Adjoint code.

In other news

Here are some other noteworthy news items ...

  1. The GEOS-Chem Support Team (GCST) is currently investigating why full-chemistry simulations done with GEOS-Chem v9-01-03 and GEOS-Chem v9-02 take longer to run than older model versions. Melissa Payer is taking the lead on this effort.

  2. We are continuing to work on the 0.25° x 0.3125° nested grid capability with the GEOS-5 “FP” (formerly known as GEOS-5.7.2) met fields. Sajeev Philip (GCST member, Dalhousie) will be extracting and regridding the met data. We are preparing to have this high-resolution nested grid capability ready for the revamped SEAC4RS mission this fall. The GCST is collaborating with Yuxuan Wang (Tsinghua), Jenny Fisher (Wollongong), Lin Zhang (Peking U.), Patrick Kim (Harvard) and others towards this end.

  3. Jeff Pierce (CSU) recently hired programmer Sal Farina to synchronize the TOMAS aerosol microphysics package with the latest GEOS-Chem code. TOMAS had been integrated into GEOS-Chem v8-03-01, but further TOMAS development lagged behind the standard GEOS-Chem.

  4. Sebastian Eastham (working w/ Steven Barrett @ MIT) has deliverd a new aircraft emissions module (AEIC) to the GCST. This new aircraft emissions package is slated to be added into GEOS-Chem v9-02, along with other emissions updates.

  5. Prasad Kasibhatla (Duke) has prepared GFED3 emissions throughout the end of 2011 (the previous data ended in 2010). The new data are stored on the Harvard server. We plan to standardize support for the extended GFED3 data as part of our "emissions update" to GEOS-Chem v9-02.

  6. Debra Weisenstein (Harvard) and Steven Barrett (MIT) are working on a state-of-the-art OCS simulation for GEOS-Chem.

  7. Colette Heald (MIT) is working with AER Corp. to install the RRTMG radiative transfer model into GEOS-Chem.

  8. We invite you to view the GEOS-Chem board on Trello.com to see the current tasks that we are working on now. We update this board whenever we complete tasks (cards are archived for future reference).

--Bob Y. 14:57, 9 January 2013 (EST)

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