Difference between revisions of "GEOS-Chem Adjoint"
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<big>'''Adjoint and Data Assimilation Working Group'''</big> | <big>'''Adjoint and Data Assimilation Working Group'''</big> | ||
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| − | + | == Historical Development == | |
| − | + | 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 ([http://www.autodiff.com/tamc TAMC], [http://people.cs.vt.edu/~asandu/Software/Kpp/ KPP]) and manual coding of both discrete and continuous adjoints. They shared many common elements yet had unique features for different applications. | |
| − | Original work on the adjoint of GEOS-Chem 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 | + | |
| − | == | + | == Current Adjoint Code == |
| − | + | 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. | |
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| − | === | + | === Features === |
| − | * | + | * Meteorological fields |
| − | + | ** GEOS-3 <i>needs testing</i> | |
| − | + | ** GEOS-4 | |
| − | + | ** GEOS-5 | |
| − | + | * model resolution | |
| − | + | ** 4 x 5 | |
| − | + | ** 2 x 2.5 <i>needs testing</i> | |
| − | + | * Forward model processes | |
| − | + | ** convection | |
| − | * | + | ** advection |
| − | * | + | ** PBL mixing |
| − | * | + | ** dry deposition |
| − | + | ** wet deposition <i> needs updating </i> | |
| − | + | ** strat / trop exchange with LINOZE <i> needs updating </i> | |
| − | + | ** NOy up fluxes <i> needs doing </i> | |
| − | + | ** aerosols | |
| − | * | + | *** inorganic aerosol thermodynamics |
| − | * | + | *** sulfate chemistry <i> needs updating </i> |
| + | *** BC | ||
| + | *** SOA, Dust, sea salt <i> needs doing </i> | ||
| + | *** aerosol surface area feedbacks <i> needs updating </i> | ||
| + | *** aerosol optical feedbacks <i> needs doing </i> | ||
| + | ** emissions | ||
| + | *** lightning NOx <i> needs updating </i> | ||
| + | *** soil NOx <i> needs updating </i> | ||
| + | *** all others | ||
| + | * Simulation modes | ||
| + | ** full chemistry | ||
| + | ** tagged CO | ||
| + | ** tagged Ox <i>needs updating</i> | ||
* Observational Operators | * Observational Operators | ||
| − | ** IMPROVE PM2.5 (NO3, SO4, OC, BC) | + | ** MOPITT CO column |
| − | ** CASTNet (NH4+) | + | ** SCIAMACHY CO column |
| − | ** GOME / SCIAMACHY NO2 column | + | ** AIRS CO column |
| + | ** IMPROVE PM2.5 (NO3, SO4, OC, BC) <i> needs updating </i> | ||
| + | ** CASTNet (NH4+) <i> needs updating </i> | ||
| + | ** GOME / SCIAMACHY NO2 column <i> needs updating </i> | ||
*** using KNMI retrieval (Henze) | *** using KNMI retrieval (Henze) | ||
*** using Dalhousie retrieval (Shim) | *** using Dalhousie retrieval (Shim) | ||
| − | ** TES NH3 | + | ** TES NH3 <i> needs updating </i> |
| + | ** TES O3 <i> needs updating </i> | ||
* Control parameters | * Control parameters | ||
| − | ** Emissions scaling factors (linear or log) | + | ** Initial Conditions scaling factors (linear or log) |
| + | ** Emissions scaling factors (linear or log) <i> needs updating </i> | ||
*** SOx, NH3, primary BC/OC: anthropogenic, natural, bioburn, biomass, volcanoes | *** SOx, NH3, primary BC/OC: anthropogenic, natural, bioburn, biomass, volcanoes | ||
| − | |||
* Adjoint sensitivities | * Adjoint sensitivities | ||
| − | ** all control parameters | + | ** all implemented control parameters |
| − | ** w.r.t Reaction Rate Parameters | + | ** w.r.t Reaction Rate Parameters <i> needs updating </i> |
| − | ** w.r.t all emissions | + | ** w.r.t all emissions <i> needs updating </i> |
| − | ** to AQ attainment metrics | + | ** to AQ attainment metrics <i> needs updating </i> |
| − | ** to spatiotemporally averaged species concentrations (e.g., arctic O3) | + | ** to spatiotemporally averaged species concentrations (e.g., arctic O3) <i> needs updating </i> |
| − | * Inverse Hessian approximation | + | * Other |
| − | * | + | ** Inverse Hessian approximation <i> needs updating </i> |
| − | * | + | ** off-diagonal covariance matrices <i> needs updating </i> |
| + | ** 3D-Var <i> needs updating </i> | ||
| − | + | Features may be qualified as: | |
| − | + | * <i>needs testing</i>: an implemented feature that we haven't fully used yet | |
| + | * <i>needs updating</i>: a feature developed with a previous branch that has yet to be updated to GEOS-Chem v8 and the merged adjoint | ||
| + | * <i>needs doing</i>: a feature nobody has tackled the adjoint of yet | ||
| − | === | + | === Primary code developers === |
| − | + | Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze | |
| − | ==== | + | === Adjoint model lead scientist === |
| − | + | Daven Henze | |
| − | + | ||
| + | == Obtaining and using the adjoint model code == | ||
| + | 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. A user's guide is available. http://puck.che.caltech.edu/%7Edaven/home/GC_adj/GC_adj_man.pdf | ||
| − | + | 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. | |
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| − | ==== | + | == 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 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. | ||
| + | |||
| + | |||
| + | == Get Involved == | ||
| + | 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 this list by sending an email to [mailto:geos-chem-adjoint-requests@seas.harvard.edu geos-chem-adjoint-requests@seas.harvard.edu] with the word subscribe in the subject or body, or you may click here for browser sign-up: https://lists.seas.harvard.edu/mailman/listinfo/geos-chem-adjoint). | ||
| + | |||
| + | Kevin Bowman organizes bimonthly conference calls concerning current adjoint model activities. | ||
| + | |||
| + | |||
| + | == Publications == | ||
| + | |||
| + | === Journal Articles === | ||
| + | |||
| + | * Kopacz, M. et al., CO source estimates as derived in an adjoint inversion from combined MOPITT, AIRS and SCIAMACHY measurements of CO columns, submitted. | ||
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* 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 | * 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 | ||
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| − | + | * 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. | |
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| − | + | * 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 | |
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| − | + | * Henze, D. K., A. Hakami and J. H. Seinfeld (2007), Development of the adjoint of GEOS-Chem, Atmos. Chem. Phys., 7, 2413-2433. | |
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| − | === | + | |
| + | === Conference proceedings === | ||
| + | * 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 | ||
Revision as of 07:08, 21 September 2009
Adjoint and Data Assimilation Working Group
Contents
Historical Development
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.
Current Adjoint Code
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.
Features
- Meteorological fields
- GEOS-3 needs testing
- GEOS-4
- GEOS-5
- model resolution
- 4 x 5
- 2 x 2.5 needs testing
- Forward model processes
- convection
- advection
- PBL mixing
- dry deposition
- wet deposition needs updating
- strat / trop exchange with LINOZE needs updating
- NOy up fluxes needs doing
- aerosols
- inorganic aerosol thermodynamics
- sulfate chemistry needs updating
- BC
- SOA, Dust, sea salt needs doing
- aerosol surface area feedbacks needs updating
- aerosol optical feedbacks needs doing
- emissions
- lightning NOx needs updating
- soil NOx needs updating
- all others
- Simulation modes
- full chemistry
- tagged CO
- tagged Ox needs updating
- 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 needs updating
- TES O3 needs updating
- Control parameters
- Initial Conditions scaling factors (linear or log)
- Emissions scaling factors (linear or log) needs updating
- SOx, NH3, primary BC/OC: anthropogenic, natural, bioburn, biomass, volcanoes
- Adjoint sensitivities
- all implemented control parameters
- w.r.t Reaction Rate Parameters needs updating
- w.r.t all emissions needs updating
- to AQ attainment metrics needs updating
- to spatiotemporally averaged species concentrations (e.g., arctic O3) needs updating
- Other
- 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
Primary code developers
Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze
Adjoint model lead scientist
Daven Henze
Obtaining and using the adjoint model code
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. A user's guide is available. http://puck.che.caltech.edu/%7Edaven/home/GC_adj/GC_adj_man.pdf
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 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.
Get Involved
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 this list by sending an email to geos-chem-adjoint-requests@seas.harvard.edu with the word subscribe in the subject or body, or you may click here for browser sign-up: https://lists.seas.harvard.edu/mailman/listinfo/geos-chem-adjoint).
Kevin Bowman organizes bimonthly conference calls concerning current adjoint model activities.
Publications
Journal Articles
- Kopacz, M. et al., CO source estimates as derived in an adjoint inversion from combined MOPITT, AIRS and SCIAMACHY measurements of CO columns, submitted.
- 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.
Conference proceedings
- 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
