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Current GEOS–Chem version

The GEOS–Chem Model: New Developments Bob Yantosca Software Engineer Atmospheric Chemistry Modeling Group Harvard University 3 rd GEOS–Chem Users’ Meeting Wednesday, April 11, 2007. Current GEOS–Chem version. Last public release: GEOS–Chem v7–03–06 (Nov 2005) This was a public release.

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Current GEOS–Chem version

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  1. The GEOS–Chem Model: New DevelopmentsBob YantoscaSoftware EngineerAtmospheric Chemistry Modeling GroupHarvard University3rd GEOS–Chem Users’ MeetingWednesday, April 11, 2007

  2. Current GEOS–Chem version • Last public release: GEOS–Chem v7–03–06 (Nov 2005)This was a public release • Current release: GEOS–Chem v7–04–12 (Mar 2006)This is an internal release • v7–04–12 contains updates in these areas: • Chemistry • Emissions • Technical issues • Met Fields (esp. GCAP) Focus on these ! • Further ongoing code development in these areas: • Met fields (esp. transition to GEOS–5) • Chemistry (new solver, cf. Philippe & Yevgenii!) • Adjoint (cf. A. Sandu et al) • Earth System Model Framework (coming soon!)

  3. ESMF Overview Summary • What is ESMF? • It’s a software framework for earth science models that is being implemented at NASA and elsewhere • http://www.esmf.ucar.edu • What ESMF will do: • It will make it easier to connect “pieces” of the same model together • It will make it easier to take “pieces” of one model and mix them with “pieces” from other models. • It connects “pieces” of models together regardless of which language the models were written in (Fortran, C, C++, etc.) • It will probably eventually reduce model development time (however, some up-front development will be needed) • What ESMF will not do: • It will NOT improve the quality of the science of a model

  4. With ESMF, you can reduce a CTM to a collection of “pluggable”black box “Components” with standard inputs & outputs ESMF library functions pass data into & out of components! Diagnostics NOTE: All of the data that flows into a component goes in through the “front door”, I.e. through argument lists. No more global common blocks! In the future, GEOS–Chem will be a configuration of ESMF-compliant components instead of a standalone model

  5. Making GEOS–Chem ESMF Compliant • GEOS–Chem is in good shape for ESMF conversion • Most new G–C code is in F90 module form • Each F90 module has INIT and CLEANUP routines • G–C is highly “methodized” • Many quantities are accessible via function calls • Complexity is moved to functions rather in main code • G–C has consistent file I/O and error handling • G–C code is very well documented • We are committed to making GEOS–Chem ESMF compliant • We have obtained funding to support code conversion • Bob Y. will collaborate with NASA/SIVO (e.g Tom Clune et al) • We will work with SIVO and contribute codes to repository • We will also be able to incorporate other ESMF components from SIVO and the greater modeling community back into GEOS–Chem

  6. Making GEOS–Chem ESMF Compliant • What GEOS–Chem users can expect • The structure of GEOS–Chem will change • Naming conventions, units, etc. will be standardized • 3rd party routines will have to be modified for ESMF compliance • File format: netCDF or HDF-EOS instead of binary • Technical Challenges • ESMF requires several libraries to be installed • ESMF is not ported to Sun platform (will be done Oct 2007) • ESMF programming docs are not very clear for new users • What would be useful is an “ESMF for beginners” tutorial that is geared specifically towards atmospheric models • GEOS–Chem users will have to adopt an ESMF-mindset • Object-oriented coding style

  7. G–C: New Developments in Chemistry • Most important update: G–C can now do SMVGEAR chemistry up to the location of the actual tropopause instead of the “annual mean tropopause”Developed by Brendan Field; Implemented by Philippe Le Sager GEOS-4 2x25 ann mean trop ht GEOS-4 2x25 dynamic trop ht, July 2001 km km Abs Diff (dynamic trop – mean trop) % Diff (dynamic trop – mean trop) Courtesy Philippe Le Sager km %

  8. G–C: New Developments in Emissions • Incorporation of several new emissions inventories • Option to use GFED2 biomass emissions for 15 gas + aerosol speciesPrasad Kasibhatla (Duke), Rokjin Park (Seoul Nat. Univ) • Option to use David Streets' regional anthro emissions for China and SE Asia (NOx, CO, SO2, NH3)Yuxuan Wang (Harvard) • Option to use EDGAR global anthro emissions (NOx, CO, SO2)Aaron Van Donkelaar (Dalhousie Univ) • Option to use BRAVOanthropogenic emissions (NOx, CO, SO2) over Northern MexicoRokjin Park, Folkert Boersma (Harvard) • David Streets’ & BRAVO are regional overlay anthro datasets. They replace whichever global anthropogenic emissions you are using (EDGAR or GEIA) in their respective geographic regions.

  9. G–C: New Developments in Emissions • Updated lightning NOx emissions, with • Near-land lightning flashes • OTD/LIS “v2” regional re-distributon (method of L. Jourdain et al) • Mid-latitude & tropics emissions follow Hudman et al 2007Lee Murray & Rynda Hudman (Harvard) *** CAVEAT: New lightning currently only implemented for GEOS–4 ***

  10. G–C: New Developments in Emissions • We are in the process of running a “matrix” of 1-yr benchmark simulations with v7–04–12 in order to determine the “best” combination of emissions options. • Run 1: “old” lightning, “old” biomass burning, “old” fossil fuel, … • Run 2:Same as Run 1, but use “new” lightning (cf. Hudman et al 2007) • Run 3:Same as Run 2, but use GFED2 biomass burning • … “old” = the same as in the previous 1-yr benchmark (v7–02–03) • From these 1-yr benchmark simulations, we will also be able to assess the the impact that the new lightning NOx emissions will have on Ozone and OH.

  11. G–C: New Technical Developments • GEOS–Chem can run on the following compiler / platform combos: • Sun X4100 (AMD/Opteron) with Sun Studio 11 compiler (NEW!) • Sun (SPARC v8 or v9) with Sun Studio 11 compiler • SGI Altix (Itanium) with Intel v9 “ifort” compiler (NEW!) • PC/Linux with Intel v9 “ifort” compiler (NEW!) • PC/Linux with Portland Group Int’l (PGI) compiler • SGI Origin with SGI MIPS v7.2 or v7.3 compiler • IBM / AIX with IBM compiler • HP/Compaq ALPHA with HP/Compaq compiler • *** any others *** ?? • The following compilers have now been de-supported: • Intel v7 “EFC” compiler for Altix/Itanium • Intel v7 “IFC” compiler for PC/Linux • NOTE: Intel “v9” ifort compiler produces much more optimal code than “EFC” compiler. GEOS–Chem runs almost 2X as fast!!!

  12. Transition to GEOS–5 What has been done so far: • GEOS–5 2005 met data has been obtained from GMAO & regridded • 0.5 x 0.667 China nested grid, 2x25, 4x5 resolution • Met field files are in binary format (convert to netCDF or HDF–EOS later) Vertical levels up to 30 km GEOS–5 native vertical resolution is 72 levels! GEOS–Chem can condense these on-the-fly down to 47 levels by lumping levels in the stratosphere together above L=36 (78 hPa) This is done for computational expediency. GEOS– 3 GEOS–4 GEOS–5 NOTE: GEOS–5 has much greater resolution in the PBL than GEOS–4!

  13. Transition to GEOS–5 • Existing TPCORE has been modified for GEOS–5 (JUST LAST WEEK!) • GEOS–5 gives you pressure at grid box edges every 6 hrs instead of allowing you to compute it as an analytic function • TPCORE had to be rewritten to accept pressure edge arrays instead • Pressure fixer also had to be rewritten to accept pressure edge arrays Yuxuan Wang &Bob Yantosca

  14. Transition to GEOS–5 • Quick full-chemistry test runs have been done with GEOS–5 • Test runs have been done with the following operations turned on: • Chemistry, Cloud Convection, Dry Deposition Wet Deposition, Emissions, PBL mixing, and Transport (aka Advection) • Caveat: Lightning needs the same treatment as GEOS–4 (to be done later) G–C w/ GEOS–5 chemically produced OH (2005/01/02) G–C w/ GEOS–5: drydep of Ox (2005/01/02) G–C w/ GEOS–5: chemically produced HO2 (2005/01/02) NOTE: don’t yet treat these as scientific results. I am showing this to demonstrate that GEOS–Chem can be run with the GEOS–5 fields through the various operations without crashing!

  15. GEOS–Chem Model Clinic • Philippe and I will be available on Friday afternoon (starts ~ 3PM) • We will answer specific questions about GEOS–Chem, GAMAP, data issues, etc.

  16. Extra Slides

  17. What is ESMF? • ESMF provides tools for turning model codes into components with standard interfaces and standard drivers • ESMF provides data structures and common utilities that components use • to organize codes • to improve performance portability • for common services such as data communications, regridding, time mgmt and message logging

  18. ESMF Superstructure Classes Schematic of an ESMF Gridded Component Input State Output State ESMF Clock Return code Each ESMF Gridded Component must have init, run, finalize routines. Init takes data from the Input state and allocates all internal data storage Run is used to invoke the user source code Finalize deallocates all internal storage. ESMF Superstructure Layer User Code Init Routine User Code Run Routine User Code Finalize Routine ESMF library function calls Internal F90 code routines Internal F90 code routines Internal F90 code routines ESMF Infrastructure Layer

  19. New Developments in Chemistry Other Minor Updates Addition of 2 extra secondary organic aerosol tracers (SOG4, SOA4). This is necessary to track the production of SOA from the rxn ISOP + OH.Developed by Daven Henze (Caltech); Implemented by Bob Yantosca Secondary organic gas tracers (SOG) are now condensed onto SO4, NH4, and NIT aerosols, for both full-chemistry and aerosol chemistry simulations.Developed by Rokjin Park (Seoul National Univ, Korea), formerly at Harvard HO2 uptake by aerosols is now turned off in the SMVGEAR mechanismDeveloped by Bastien Sauvage (Dalhousie U.); Implemented by Bob Yantosca.

  20. G–C: New Met Field Developments • The following met fields have now been de-supported: • GEOS–1 • GEOS–STRAT • We now have 20+ years of GEOS–4 met data on disk, thus obviating the need to use GEOS–1 and GEOS–STRAT. • GEOS–5 will also have multiple years. • The following updates have been added for GCAP met: • Archive extra physical quantities in GCAP met field files so that GEOS–Chem can use the MEGAN biogenic inventory. • Bug fix: have GEOS–Chem skip over Feb 29th when using GCAP met.(GCAP years are always 365 days.) • Bug fix: treat negative detrainment as an entrainment in the cloud convection scheme. This will preserve mass for long-lived species like CO2. (cf. Shiliang Wu)

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