Adjoint and Data Assimilation Working Group
- 1 Contact information
- 2 Historical Development
- 3 Current Forward Model Code
- 4 Current Adjoint Code
- 5 Documentation
- 6 Distribution and Use
- 7 Giving credit for using the adjoint model
- 8 Current GEOS-Chem Adjoint Research Projects (please add yours!)
- 9 Get Involved
- 10 Publications
|Adjoint Working Group Chair||Kevin Bowman|
|Adjoint Model Scientist||Daven Henze|
|Adjoint Working Group email email@example.com|
|To subscribe to email list||Send email to firstname.lastname@example.org|
|To unsubscribe from email list||Send email to email@example.com|
Original work on the adjoint of GEOS-Chem v6 began in 2003, focusing on the adjoint of the offline aerosol simulation. By 2005, the adjoint was expanded to include a tagged CO simulation and a full chemistry simulation; an adjoint of GEOS-Chem v7 was also developed in the following years. Each of these branches of the adjoint code were been constructed in a hybrid fashion using a combination of automatic differentiation software (TAMC, KPP) and manual coding of both discrete and continuous adjoints. They shared many common elements yet had unique features for different applications.
During the summer of 2009, the existing branches were merged and updated to bring the adjoint into alignment with the latest release of GEOS-Chem, v8-02-01. This merged adjoint model is now the standard adjoint code into which all further development efforts will be placed.
Current Forward Model Code
The forward model on which the adjoint is based corresponds to GEOS-Chem v8-02-01 with the following updates:
- KPP solver for gas-phase chemistry (as in GCv8-02-03)
- Implement Bond 2007 BC/OC emissions (as in GCv8-02-02)
- Apply bug fixes from GCv8-02-02 listed here
- Apply bug fixes from GCv8-02-03 listed here
- Apply bug fixes from GCv8-02-04 listed here
All bug fixes and model updates that have been ported from the forward model are now listed at the top of inverse_driver.f. For example:
!Revision 1.31 2011/02/23 00:08:47 daven !UPDATES in forward model: ! - add diag59 (lz, 11/18/10) ! - GCv8-02-04: add EPA/NEI05. ! - completely update scale_anthro_mod.f to GCv9-01-01 ! - completely update epa_nei_mod.f to GCv9-01-01 ! - add nei2005_anthro_mod.f to GCv9-01-01 ! - completely update error_mod.f to GCv9-01-01 ! !BUG FIXES in forward model: ! - GCv8-02-03: Corrected_Bond_et_al_BC.2FOC_emissions ! - GCv8-02-04: Bug_fix_in_emfossil.f_for_0.5_x_0.666_nested_grid_tagged-CO_option ! - GCv8-03-02: Fix_for_EPA.2FNEI_2005_emissions ! - GCv8-03-02: Minor_fixes_in_gamap_mod.f ! - GCv9-01-01: Bug_fix_for_biofuels_in_EPA.2FNEI05 ! - GCv?-??-??: Add scaling of aromatic emissions over the US. (hotp, 11/23/09) ! - GCv9-01-01: Important_bug_fixes_for_ship_emissions ! - GCv9-01-01: Fix_to_prevent_div-by-zero_in_sulfate_mod.f ! - GCv9-01-02: Double_counting_of_biofuel_emissions_over_Asia ! - GCv9-01-02: fix SET_TINDEX for ND17, 18, 38, 39 so that all wet diagnostics get written out (dkh, 02/16/11)
Current Adjoint Code
- Meteorological fields
- GEOS-3 needs testing
- model resolution
- 4 x 5
- 2 x 2.5
- Asia nested (for tagged CO only)
- Forward model processes
- PBL mixing
- dry deposition
- wet deposition
- strat / trop exchange with LINOZ (GEOS-4 implementation of LINOZ needs further testing )
- NOy up fluxes
- inorganic aerosol thermodynamics with RPMARES
- inorganic aerosol thermodynamics with ISORROPIA in progress
- sulfate chemistry
- SOA, Dust, sea salt needs doing
- aerosol surface area feedbacks needs updating
- aerosol optical feedbacks needs doing
- all standard emissions included
- Simulation modes
- full chemistry
- tagged CO
- tagged Ox
- methane in progress
- Observational Operators
- MOPITT CO column
- SCIAMACHY CO column
- AIRS CO column
- IMPROVE PM2.5 (NO3, SO4, OC, BC) needs updating
- CASTNet (NH4+) needs updating
- GOME / SCIAMACHY NO2 column needs updating
- using KNMI retrieval (Henze)
- using Dalhousie retrieval (Shim)
- TES NH3
- TES O3
- GOSAT CO2
- MLS O3 and TES CO2 in progress
- Control parameters
- Initial Conditions scaling factors (linear or log)
- Emissions scaling factors (linear or log)
- NH3, primary BC/OC, SO2: anthropogenic, natural, bioburn, biomass, ship
- NOx: soil, aircraft, anthropogenic, biofuel, bioburn
- Lightning NOx: injection height, yield in progress
- all other gas-phase tracers: anthropogenic, biofuel, bioburn
- Adjoint sensitivities
- w.r.t. all implemented control parameters
- w.r.t Reaction Rate Parameters
- w.r.t all emissions
- of AQ attainment metrics needs updating
- of spatiotemporally averaged species concentrations (e.g., arctic O3)
- Inverse Hessian approximation needs updating
- off-diagonal covariance matrices needs updating
- 3D-Var needs updating
Features may be qualified as:
- needs testing: an implemented feature that we haven't fully used yet
- needs updating: a feature developed with a previous branch that has yet to be updated to GEOS-Chem v8 and the merged adjoint
- needs doing: a feature nobody has tackled the adjoint of yet
- in progress: a feature currently under development
- in pipeline: a feature which has been submitted and awaiting integration into the CVS repository
Primary code developers
Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze
Adjoint model lead scientist
- Nicolas Bousserez reported a problem with compiling the GEOS-Chem adjoint with OpenMP under IFORT 11.
- There is a bug in the forward model implementation of variable tropopause which can cause unstable adjoints. Recommend turning off variable tropopause for all full chemistry adjoint runs.
A user's guide is available. http://adjoint.colorado.edu/%7Edaven/gcadj_std/GC_adj_man.pdf
Meemong Lee has created a detailed flowchart of the inverse model code structure. http://adjoint.colorado.edu/~daven/gcadj_std/flowchart.pdf
Distribution and Use
Code for the adjoint is distributed through a CVS server located at adjoint.colorado.edu. Contact Daven Henze to obtain an account on the server.
Even if your office mate has a copy of the code, the best way to obtain the model is to get a CVS account for yourself and download a version from the repository. So please do not copy code directly from others or pass the code along to third parties. This vastly helps with tracking developments and keeping up with model updates.
Use of the adjoint model code follows standard practice for GEOS-Chem. It is expected that any developments that come of individual applications based on this community model will eventually be given back to the community by incorporation of new developments into the standard adjoint code. New development should be submitted to Daven Henze for inclusion in the standard adjoint model code.
Giving credit for using the adjoint model
We aim to make distribution of adjoint model code as immediate as possible. A consequence is that many features may not yet be publicly documented. Therefore, giving code developers due credit is of utmost importance. At this point, any use of the GEOS-Chem model adjoint should include as co-authors the primary developers: Daven Henze, Monika Kopacz, Kumaresh Singh and Changsub Shim. In trade, we provide user support. As the model matures and user support become less of an issue, these requirements will be relaxed.
Authors of new additions to the standard code will be given due credit on the first round of publications to come of their development. Hence, additional co-authors may also be required if the application uses features that are newly developed by additional developers.
Lastly, it is requested that users of the GEOS-Chem adjoint consider offering co-author ship to several additional scientists who have contributed to the adjoint code support and progress, such as Kevin Bowman, Adrian Sandu and Daniel Jacob.
Overall, if you have any questions about authorship, even for a conference presentation, please contact Daven Henze.
Current GEOS-Chem Adjoint Research Projects (please add yours!)
|User Group||Description||Contact Person|
|CU Boulder||Aerosol precursors, CO2, O3; general adjoint code maintenance||Daven Henze|
|Purdue University||Methane (SICAMACHY, AIRS and IASI)||Jinyun Tang|
|MIT||Aircraft emissions||Jamin Koo|
|Princeton||BC sensitivities, general adjoint code development||Monika Kopacz, mkopacz [at] princeton.edu|
|Dalhousie University||Lightning NOx emissions and impact on tropical ozone using the adjoint||Nicolas Bousserez|
|JPL||Microwave Limb Sounder (MLS) Ozone assimilation||Meemong Lee|
|JPL||TES ozone assimilation/attribution of ozone radiative forcing||Kevin Bowman|
|University of Edinburgh||Quantifying the impact of boreal forest fires on tropospheric oxidants over the Atlantic||Mark Parrington|
|US EPA||Integration with economic models for future emission inventory scenario development||Farhan Akhtar|
|Peking University||Satellite constraints on VOC emissions||May Fu|
|CU Boulder||Aerosol precursor emissions||Alex Turner|
|Purdue University||Feedback between terrestrial ecosystem processes and atmospheric co2 signals||Qing Zhu|
Support and development of the GEOS-Chem adjoint has clearly become a broad undertaking. In attempt to focus such developments, we've created a GC-adjoint mailing list. If you wish to become involved, you should add yourself to the GEOS-Chem adjoint email list by following the instructions posted here
Kevin Bowman organizes bimonthly conference calls concerning current adjoint model activities.
- Singh, K., Jardak, M., Sandu, A., Bowman, K., Lee, M., and Jones, D.: Construction of non-diagonal background error covariance matrices for global chemical data assimilation, Geosci. Model Dev. Discuss., 3, 1783-1827, doi:10.5194/gmdd-3-1783-2010, 2010. http://www.geosci-model-dev-discuss.net/3/1783/2010/gmdd-3-1783-2010.html
- Kopacz, M., D. L. Mauzerall, J. Wang, E. M. Leibensperger, D. K. Henze, and K. Singh, Origin and radiative forcing of black carbon transported to the Himalayas and Tibetan Plateau, Atmos. Chem. Phys. Discuss., 10, 21615-2165. http://www.atmos-chem-phys.net/10/855/2010/acp-10-855-2010.html
- Kopacz, M., D.J. Jacob, J.A. Fisher, J. A. Logan, L. Zhang, I. A. Megretskaia, R. M. Yantosca, K. Singh, D. K. Henze, J. P. Burrows, M. Buchwitz, I. Khlystova, W. W. McMillan, J. C. Gille, D. P. Edwards, A. Eldering, V. Thouret, and P. Nedelec (2010): Global estimates of CO sources with high resolution by adjoint inversion of multiple satellite datasets (MOPITT, AIRS, SCIAMACHY, TES), Atmos. Chem. Phys., 10, 855-876. http://www.atmos-chem-phys.net/10/855/2010/acp-10-855-2010.pdf
- Kopacz, M., D. J. Jacob, D. K. Henze, C. L. Heald, D. G. Streets, and Q. Zhang (2009), A comparison of analytical and adjoint Bayesian inversion methods for constraining Asian sources of CO using satellite (MOPITT) measurements of CO columns, J. Geophys. Res., doi:0.1029/2007JD009264. http://acmg.seas.harvard.edu/publications/KopaczJGR2009_2007JD009264.pdf
- Henze, D. K., J. H. Seinfeld and D. T. Shindell (2009), Inverse modeling and mapping U.S. air quality influences of inorganic PM2.5 precursor emissions with the adjoint of GEOS-Chem, Atmos. Chem. Phys., 9, 5877-5903.
- Zhang, L., D. J. Jacob, M. Kopacz, D. K. Henze, K. Singh, and D. A. Jaffe (2009), Intercontinental source attribution of ozone pollution at western U.S. sites using an adjoint method, Geophys. Res. Lett., 36, L11810, doi:10.1029/2009GL037950
- Henze, D. K., A. Hakami and J. H. Seinfeld (2007), Development of the adjoint of GEOS-Chem, Atmos. Chem. Phys., 7, 2413-2433.
- Adjoint inversion of CO sources using combined MOPITT, SCIAMACHY and AIRS CO columns, presented by Monika Kopacz at the COSPAR Scientific Assembly, Montreal, July 18, 2008. http://acmg.seas.harvard.edu/presentations/powerpoints/mak2008/COSPAR_MKopacz_July2008.ppt
- Singh, K., P. Eller, A. Sandu, D. K. Henze, K. Bowman, M. Kopacz, and M. Lee (2009), Towards the construction of a standard geos-chem adjoint model, ACM High Performance Computing Conference.
- Kopacz, M., Mauzerall, D.L., Leibensperger, E.M., Wang, J., Henze, D.K., Singh, K., Shim, C. Identifying the origin and estimating the radiative forcing of BC in the Himalayas: an analysis using the global GEOS-Chem adjoint model, European Geophysical Union meeting, Vienna, May 4, 2010.
- Kopacz, M., Jacob, D.J., Fisher, J.A., Logan, J.A., Zhang, L., Megretskaia, I.A., Yantosca, R.M., Singh, K., Henze, D.K., Burrows, J.P., Buchwitz, M., Khlystova, I., McMillan, W.W., Gille, J.C., Edwards, D.P., Eldering, A., Thouret, V., Nedelec, P. Global estimates of CO sources with high resolution by adjoint inversion of multiple satellite datasets (MOPITT, AIRS, SCIAMACHY, TES), European Geophysical Union meeting, Vienna, May 7, 2010.
- Tang, J., Zhuang, Q. and Xiong, X. (2010), 4D-Var inversion of atmospheric methane fluxes by assimilating SCIAMACHY and AIRS satellite retrievals, AGU, Dec. 18, 2010, http:/web.ics.purdue.edu/~tang16/agu2010_tang.ppt
- Bousserez, N., R. V. Martin, K. W. Bowman, D.K. Henze, M. Kopacz, K. Singh, C. Shim, C. Wespes, Improving the lightning NOx source using satellite observations: a 4D-var analysis approach, AGU, Dec., 2010, http://myweb.dal.ca/nc689777/AGU_liNOx_poster_final.pdf