GEOS-Chem Adjoint Model: Difference between revisions

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|[mailto:tuang372@gmail.com Li Tuang]
|[mailto:tuang372@gmail.com Li Tuang]
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|Georgia Institute of Technology
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|[mailto:chenylis10@gmail.com Yilin Chen]
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Revision as of 14:21, 26 July 2019

Adjoint Model and Data Assimilation Working Group

Contact information

Adjoint Model Scientist Daven Henze
Adjoint Model and Data Assimilation
Working Group Co-Chairs
GEOS-Chem Adjoint support team
Adjoint Working Group email list geos-chem-adjoint [at] g.harvard.edu
To subscribe to email list Either
  • Send an email to geos-chem-adjoint+subscribe [at] g.harvard.edu

Or

To unsubscribe from email list Either
  • Send an email to geos-chem-adjoint+unsubscribe [at] g.harvard.edu

Or

--Bob Y. (talk) 15:54, 21 August 2015 (UTC)

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.

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.

Forward Model Code

The forward model on which the adjoint is based originally corresponded to GEOS-Chem v8-02-01. It was subsequently updated as follows:

  • 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 were previous listed at the top of inverse_driver.f. Since then the code has been kept up to date with bug fixes and some forward model updates in v9 and v10. We have now switched to documenting the code development cycle here in the wiki, see the following section.

Code Versions, Bug Fixes and Developments

Current GEOS-Chem adjoint version released

Previous GEOS-Chem adjoint versions released

Summary of Main Adjoint Code Supported Features

Features

  • Meteorological fields
    • GEOS-3 needs testing
    • GEOS-4
    • GEOS-5
    • GEOS-FP
    • MERRA and MERRA2 in progress
  • model resolution
    • 4 x 5
    • 2 x 2.5
    • 0.5 x 0.666
    • 0.25 x 0.3125
    • Nested China and North America
    • Small Domain China and North America
  • Forward model processes
    • convection
    • advection
    • PBL mixing
    • dry deposition
    • wet deposition
    • strat / trop exchange with LINOZ and new GMI strat chem (v9-01-03)
    • NOy up fluxes (now replaced with new GMI strat chem)
    • aerosols
      • inorganic aerosol thermodynamics with RPMARES
      • inorganic aerosol thermodynamics with ISORROPIA in progress
      • sulfate chemistry
      • BC
      • SOA, Dust, sea salt needs doing
      • aerosol surface area feedbacks needs updating
      • aerosol optical feedbacks needs doing
    • emissions
      • all standard emissions included
  • Simulation modes
    • full chemistry
    • tagged CO
    • tagged Ox
    • CH4
    • offline aerosols (for BC and dust only)
    • CO2
  • Observational Operators
    • MOPITT CO column
    • SCIAMACHY CO column
    • AIRS CO column
    • IMPROVE BC
    • CASTNet (NH4+) needs updating
    • GOME / SCIAMACHY NO2 column needs updating
      • using KNMI retrieval (Henze)
      • using Dalhousie retrieval (Shim)
    • SCIAMACHY/OMI NO2
      • using Dalhousie retrieval (Bousserez, Padmanabhan)
    • 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)
  • Other
    • Inverse Hessian approximation
    • 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

Daven Henze


Resources

User's guide

A User's Guide v35 is available. User's Guide v35

Previous version v32-v33 available at User's Guide v32

Quick Introduction to GitLab is available at GitLab Tutorial

The forward version of the code is based on v9-02 here is the User's Guide

Code flowchart

Meemong Lee has created a detailed flowchart of the inverse model code structure. http://adjoint.colorado.edu/~daven/gcadj_std/flowchart.pdf

Plotting tools

Some IDL and MATLAB routines for plotting benchmark results. http://adjoint.colorado.edu/~daven/gcadj_std/tools.tar.gz

Background papers and presentations

Several articles and presentations (including a GC adjoint modeling clinic overview from IGC5) providing background information about adjoints. http://adjoint.colorado.edu/~daven/gcadj_std/adj_articles.tar.gz

Distribution and Use

Code for the adjoint is distributed through GITLAB, a web interface connected to a GIT server located at adjoint.colorado.edu. You can access GITLAB at http://adjoint.colorado.edu:8080 after your account is created. Here is our Quick Start Guide.

Even if your office mate has a copy of the code, the best way to obtain the model is to get an 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.

Using GIT gives the users the ability to change the code and commit their changes without affecting the main repository hosted at adjoint.colorado.edu. Users can work with their modified versions of the code and even create their own tags because GIT acts as a local repository. When ready to submit your update to the community just create a new branch with your modifications. Send an email Daven Henze explaining your contributions and we'll do our best to include them as soon as possible.

Quick guide to GIT

As of version 34 we started using git versioning system and the GitLab web interface. We prepared GitLab Tutorial to help users get used to the web interface and git. We recommend first taking a look at GIT manual to get a general feel for how this tools works (e.g., GIT Documentation or GIT Manual Page).


Useful GIT commands:

Initial download: 

git clone ssh://git@adjoint.colorado.edu/yanko.davila/gcadj_std.git

Status of project vs the current repository: 

git status

Check difference of files (differences have colors for easy reading) 

git diff --color <wildcard> [<wildcard>] <path>/foo_mod.f

Checkout specific version 

git checkout <wildcard>

Replacing a file with the newest version from the repository: 

git checkout origin/master -- <path>/foo_mod.f

Merging changes in a file: (Reference) 

git merge -m <wildcard>

Comitting 

git commit -a

Tagging a version 

git tag -a TAGNAME

Deleting a tag 

git tag -d TAGNAME
git push origin :refs/tags/TAGNAME

Saving changes to repository 

git push

Saving tags to repository 

git push --tags

List the history of a file: 

git log -- <path>/foo_mod.f

Add a file to the repository 

git add <file_name>

Delete a file from the repository 

git rm <file_name>

Determine current version 

git show HEAD [ | grep commit]

Download remote changes, rewind your local branch, then replays all your changes over the top of your current branch one by one, until you’re all up to date. 

git pull --rebase

There are several wildcards that you can use on git for example:
"origin/master" - Latest version on the repository
"HEAD" - Latest version as of your last download
"v33i" - Specific TAG, find all tag names on GitLab
"32d5c926e" - Specific COMMIT, find all commit numbers on GitLab

Here is the foward model documentation of git.

Backward compatibility (CVS)

For people using old version of the code we still have active our CVS repository, but note that the latest version on CVS is v33i-patch2. Here you can find our Quick Guide to CVS

Crediting GEOS-Chem adjoint developers

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.

Authors of new additions to the standard code should be offered co-authorship on the first round of presentations and publications to come of their development. Features currently falling in this category and their developers are:

  • (v35j) MOPITT CO Observation operator. Zhe Jiang; Yanko Davila, CU Boulder.
  • (v35j) OMI SO2, OMI NO2 and TES O3 Observation operators. Martin Keller, U Toronto; Yi Wang, U-Iowa; Yanko Davila, CU Boulder.
  • (v35j) MODIS radiance observation operators, Xiaoguang Xu and Jun Wang, U-Iowa.
  • (v35) HTAP Emissions Inventory. Kateryna Lapina, Daven Henze and Yanko Davila, CU Boulder.
  • (v35) NEI2008 Emissions Inventory. Katie Travis; Fabien Paulot, Harvard; Hyungmin Lee, and Daven Henze, CU Boulder.
  • (v35) Deposition based cost function. Fabien Paulot, Harvard; Daven Henze and Yanko Davila, CU Boulder.
  • (v34) Implementation of the sensitivity to reaction rate constants. Developers: Hyungmin Lee, CU Boulder; Thomas ; Fabien Paulot (Harvard); Daven Henze, CU Boulder and Yanko Davila, CU Boulder.
  • (v34) ISOROPIA II adjoint. Developer: Shannon Capps, EPA.
  • (v34) Off-diagonal covariance error matrices implementation. Developers: Nicolas Bousserez, CU Boulder; Kumaresh; Yanko Davila, CU Boulder.
  • (v32) Nested full chemistry adjoint. Developers: Zhe Jiang, University of Toronto; Daven Henze, CU Boulder.


Citation of the appropriate journal articles for mature developments is also encouraged, as well as considering aspects of co-authorship for the forward model.

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
Anyang University Aerosol emission modeling in East Asia Youn Seo Koo
CRAES source attribution of PM in eastern China Wei Peng
CU Boulder Aerosol precursors, CO2, O3; general adjoint code maintenance Daven Henze
CU Boulder Inverse modeling/optimization: variational source inversions, posterior error estimates in high-dimension; general adjoint code maintenance Nicolas Bousserez
CU Boulder Constraints on Aerosol Sources Zhen Qu
CU Boulder Source Receptor Relationships in Air Quality Omar Nawaz
Dalhousie University Mass balance vs adjoint approaches for top-down constraints on NOx emissions Matthew Cooper
Dalhousie University Trends in OC and BC emissions over the US Nathaniel Egan-Pimblett
Dalhousie University Sensitivity of global PM2.5-induced mortality to emissions Colin Lee
Dalhousie University Top-down constraints on NH3 emissions Chi Li
Dalhousie University Global contribution to the black carbon in the Arctic Junwei Xu
Drexel ISORROPIA adjoint development; NH3 assimilation; cloud droplet sensitivities Shannon Capps
Harvard Methane Bram Maasakkers, Melissa Sulprizio
Harvard Harvard Emissions Component (HEMCO) Christoph Keller
Harvard VOC emissions in N.A. constrained by satellite HCHO Jennifer Kaiser
Harvard Tradeoffs between air quality and economic outcomes Sebastian D Eastham
JAMSTEC Multiple-constituent satellite data assimilation Kazuyuki Miyazaki
JPL 3D-var Microwave Limb Sounder (MLS) and Tropospheric Emission Spectrometer (TES) ozone assimilation Meemong Lee
JPL TES ozone assimilation/attribution of GHG radiative forcing Kevin Bowman
JPL Carbon Monitoring System Flux (CMS-Flux) 4D-var and LETKF assimilation Kevin Bowman
JPL Adjoint sensitivity analysis for satellite constellation design Kevin Bowman
MIT Air quality, aircraft emissions and sensitivities Kingshuk Dasadhikari
MIT Air quality, aircraft emissions and sensitivities Irene Dedoussi
Nanjing University Inverse modeling of terrestrial ecosystem carbon flux Hengmao Wang
Nazarbayev University Emissions influences on NO_2 columns Mehdi Torkmahalleh
NCAR Adjoint analysis for carbon monoxide and ozone Zhe Jiang
Peking University Satellite constraints on VOC emissions May Fu
Peking University Source attributions of tropospheric ozone over North China Jintai Lin
Peking University Satellite Health impact analysis of China interregional pollution trade Liu Yang
Peking University Emissions and chemistry of VOCs in China. Qi Chen
Purdue University Feedback between terrestrial ecosystem processes and atmospheric CO2 signals Qing Zhu
Purdue University Feedback between aquatic ecosystem processes and atmospheric CH4 signals Zeli Tan
Seoul National University VOC emission constraints over Korea using OMI satellite retrieval and DC-8 flight measurements from KORUS-AQ Hyung-Min Lee
Seoul National University Emissions and chemistry of aerosols in East Asia Jaein Jeong
Tsinghua University Inverse modeling of anthropogenic emissions over East Asia Qiang Zhang
Tsinghua University Nested-gird simulations with the adjoint model Nan Yang
UCLA Constrain black carbon emission Ling Qi
UCLA source attribution of ozone in the western U.S. Mei Gao
University of Edinburgh Ozone sensitivity in biomass burning plumes Douglas Finch
University of Florida Nitrogen deposition related to climate strategy projections with GCAM Colleen Baublitz, Barron H. Henderson
University of Iowa Multiple-sensor (MODIS, MISR, OMI, etc.) constraints of aerosol emissions and application for AQ forecast; OSSE for future satellite missions Jun Wang, Yi Wang
University of Minnesota Inverse modeling of VOC sources based on TES and IASI measurements Kelley Wells, Dylan Millet
University of Minnesota & CU Boulder Inverse modeling of N2O sources Dylan Millet, Daven Henze
University of Toronto Methane inverse modeling Ilya Stanevich
University of Toronto Sensitivity of ozone and CO to precursor emissions Cynthia Whaley
University of Toronto Data assimilation of atmospheric CO and CO2 Tailong He
University of Wisconsin CO2 assimilation and forecast & Temperature profile retrieval Wenguang Bai
University of Wollongong Sensitivity of ozone and adjoint analysis of CO over Australasia. Rebecca Buchholz
USTC assimilation & sensitivies of CO2 Li Tuang
Georgia Institute of Technology NH3 emissions Yilin Chen

Publications

Journal Articles

  • In press or sumbitted
    • Cao, H., T.-M. Fu, L. Zhang, D. K. Henze, C. Chan Miller, C. Lerot, G. González Abad, I. De Smedt, Q. Zhang, M. van Roozendael, K. Chance, J. Li, J. Y. Zheng, Y. H. Zhao, Adjoint inversion of Chinese non-methane volatile organic compound emissions using space-based observations of formaldehyde and glyoxal, Atmos. Chem. Phys. Discuss., https://doi.org/10.5194/acp-2017-1136, in review.
    • Chen, C., O. Dubovik, D. K. Henze, T. Lapyonak, M. Chin, F. Ducos, P. Litvinov, X. Huang, L. Li, Retrieval of desert dust and carbonaceous aerosol emissions over Africa from PARASOL/GRASP observations, submitted.
    • Zhao, H., Q. Zhang, S. J. Davis, X. Li, Y. Liu, G. Geng, M. Li, B. Zheng, H. Huo, L. Zhang, D. K. Henze, K. He, Inequality of household consumption and air pollution deaths in China, submitted.
    • Nakarmi, A., B. Sharma, U. S. Rajbhandari, A. Prajapati, C. S. Malley, J. C. I. Kuylenstierna, H. W. Vallack, D. K. Henze, A. Panday, Mitigating the impacts of air pollutants in Nepal and climate co-benefits: A scenario-based approach, submitted.
  • 2018
    • Wells, K. C., D. B. Millet, N. Bousserez, D. K. Henze, T. J. Griffis, S. Chaliyakunnel, E. J. Dlugokencky, E. Saikawa, G. Xiang, R. G. Prinn, S. O'Doherty, D. Young, R. F. Weiss, G. S. Dutton, J. W. Elkins, P. B. Krummel, R. Langenfelds, L. P. Steele (2018), Top-down constraints on global N2O emissions at optimal resolution: application of a new dimension reduction technique, Atmos. Chem. Phys., 18, 735-756, https://doi.org/10.5194/acp-18-735-2018.
    • Zhang, L., Y. Chen, Y. Zhao, Y. D. K. Henze, L. Zhu, Y. Song, F. Paulot, X. Liu, Y. Pan, B. Huang (2018), Agricultural ammonia emissions in China: reconciling bottom-up and top-down estimates, Atmos. Chem. Phys., 18, 339-355, https://doi.org/10.5194/acp-18-339-2018.
  • 2017
    • Xu, X., J. Wang, Y. Wang, D. K. Henze, L. Zhang, G. A. Grell, S. McKeen. and B. Wielicki (2017), Sense Size-Dependent Dust Loading and Emission from Space Using Reflected Solar and Infrared Spectral Measurements: An Observation System Simulation Experiment, J. Geophys. Res. Atmos., 122, 8233-8254, doi: 10.1002/2017JD026677.
    • Lacey F. G., E. A. Marais, D. K. Henze, C. J. Lee, A. van Donkelaar, R. V. Martin, M. P. Hannigan, C. Wiedinmyer, Improving present day and future estimates of anthropogenic sectoral emissions and the resulting air quality impacts in Africa, Faraday Discuss., 200, 397-412.
    • Cui, Y., J. Brioude, W. M. Angevine, J. Peischl, S. A. McKeen, S-W. Kim, J. Neuman, D. K. Henze, N. Bousserez, M. Fischer, S. Jeong, H. Michelsen, R. P. Bambha, Z. Liu, G. W. Santoni, B. Duabe, E. Kort, G. Frost, T. B. Ryerson, S. C. Wofsy, M. Trainer (2017). Top-down estimate of methane emissions in California using a mesoscale inverse modeling technique: The San Joaquin Valley, J. Geophys. Res. Atmos., 122, 3686--3699, doi:10.1002/2016JD026398, online.
    • Cooper, M., R. V. Martin, A. Padmanabhan, and D. K. Henze (2017), Comparing mass balance and adjoint methods for inverse modeling of nitrogen dioxide columns for global nitrogen oxide emissions, J. Geophys. Res. Atmos., 122, 4718-4734, doi:10.1002/2016JD025985 online.
    • Bousserez, N. and D. K. Henze (2017), Optimal and scalable methods to approximate the solutions of large-scale Bayesian problems: Theory and application to atmospheric inversions and data assimilation, Q. J. R. Met. Soc., doi:10.1002/qj.3209, online.
  • 2016
    • Wang, Y., J. Wang, X. Xu, D. K. Henze, Y. Wang, Z. Qu (2016), A new approach for monthly updates of anthropogenic sulfur dioxide emissions from space: implications for air quality forecasts, Geophys. Res. Lett., 43, 9931–9938.
    • Lee, H.-M., F. Paulot, D. K. Henze, K. Travis, D. J. Jacob, L. H. Pardo, B. Schichtel (2016), Sources of nitrogen deposition in Federal Class I areas in the US, Atmos. Chem. Phys, 16, 525-540, doi:10.5194/acp-16-1-2016
    • Zhang, L., J. Shao, X. Lu, Y. Zhao, Y. Hu, D. K. Henze, H. Liao, S. Gong, Q. Zhang (2016), Sources and processes affecting fine particulate matter pollution over North China: an adjoint analysis of the Beijing APEC period, Environ. Sci. Technol., 50 (16), 8731-8740, doi:10.1021/acs.est.6b03010
    • Bousserez, N., D. K. Henze, B. Rooney, A. Perkins, K. J. Wecht, A. J. Turner, V. Natraj, J. R. Worden, Constraints on methane emissions in North America from future geostationary remote sensing measurements, Atmos. Chem. Phys., 16, 6175-6190, 2016, https://doi.org/10.5194/acp-16-6175-2016
    • Tan, Z., Q. Zhuang, D. K. Henze, C. Frankenberg, E. Dlugokencky, C. Sweeney, A. J. Turner, M. Sasakawa, T. Machida, Inverse modeling of pan-Arctic methane emissions at high spatial resolution: what can we learn from assimilating satellite retrievals and using different process-based wetland and lake biogeochemical models?, Atmos. Chem. Phys., 16, 12649–12666, doi:10.5194/acp-16-12649-2016.
  • 2015
    • Zhang, L., L. Licheng, Y. Zhao, S. Gong, X. Zhang, D. K. Henze, S. L. Capps, T.-M. Fu, Q. Zhang, Source attribution of particulate matter pollution over North China with the adjoint method, Environ. Res. Lett. 10 084011.
    • Zhao, Y. H., L. Zhang, Y. P. Pan, Y. S. Wang, F. Paulot, and D. K. Henze, Atmospheric nitrogen deposition to the northwestern Pacific: seasonal variation and source attribution, submitted.
    • Lapina, K., D. K. Henze, J. B. Milford, C. Cuvelier, and M. Seltzer, Implications of RCP Scenarios for future changes in vegetative exposure to ozone in the Western U.S., Geophys. Res. Let., Atmos. Chem. Phys., 15, 10905-10924, 2015, https://doi.org/10.5194/acp-15-10905-2015
    • Whaley, C. H., K. Strong, D. B. A. Jones, T. W. Walker, Z. Jiang, D. K. Henze, M. Cooke, C. A. McLinden, M. Pommier, R. L. Mittermeier, P. F. Fogal, Improvements to our understanding of urban ozone air pollution: Sources of Toronto-area ozone during poor air quality events, J. Geophys. Res. Atmos., 120, 11,368–11,390, doi:10.1002/2014JD022984.
    • Liu, J., Bowman, K., and Henze, D., Source-receptor relationships of column-average CO2 and implications for the impact of observations on flux inversions., J. Geophys. Res. Atmos., 120,5214–5236, doi:10.1002/2014JD022914
    • Turner, A. J. and D. J. Jacob, Balancing aggregation and smoothing errors in inverse models, Atmos. Chem. Phys., 15, 7039-7048, 2015, https://doi.org/10.5194/acp-15-7039-2015
    • Turner, A. J., D. J. Jacob, K. J. Wecht, J. D. Maasakkers, S. C. Biraud, H. Boesch, K. W. Bowman, N. M. Deutscher, M. K. Dubey, D. W. T. Griffith, F. Hase, A. Kuze, J. Notholt, H. Ohyama, R. Parker, V. H. Payne, R. Sussmann, V. A. Velazco, T. Warneke, P. O. Wennberg, and D. Wunch, Estimating global and North American methane emissions with high spatial resolution using GOSAT satellite data, Atmos. Chem. Phys., 15, 7049-7069, 2015,https://doi.org/10.5194/acp-15-7049-2015
    • Zhang, L., D. K. Henze, G. A. Grell, G. R. Carmichael, N. Bousserez, Q. Zhang, J. Cao, O. Torres, C. Ahn, Z. Lu, Y. Mao, Constraining black carbon aerosol over Southeast Asia using OMI aerosol absorption optical depth and the adjoint of GEOS-Chem, Atmos. Chem. Phys., 15, 10281-10308, doi:10.5194/acp-15-10281-2015.
    • Patrick S. Kim, Daniel J. Jacob, Loretta J. Mickley, Shannon N. Koplitz, Miriam E. Marlier, Ruth S. DeFries, Samuel S. Myers, Boon Ning Chewf, Yuhao H. Mao, Sensitivity of population smoke exposure to fire locations in Equatorial Asia, doi:10.1016/j.atmosenv.2014.09.045
    • Deng, F., D. B. A. Jones, T. W. Walker, M. Keller, K. W. Bowman, D. K. Henze, R. Nassar, E. A. Kort, S. C. Wofsy, K. A. Walker, A. E. Bourassa, and D. A. Degenstein, Sensitivity analysis of the potential impact of discrepancies in stratosphere-troposphere exchange on inferred sources and sinks of CO2, Atmos. Chem. Phys. Discuss., 15, 10813-10851, doi:10.5194/acpd-15-10813-2015.
    • Jiang, Z., D. B. A. Jones, J. R. Worden, H. M. Worden, D. K. Henze, Y. X. Wang, Regional data assimilation of multi-spectral MOPITT observations of CO over North America, Atmos. Chem. Phys. Discuss., 15, 5327-5358, doi:10.5194/acpd-15-5327-2015.
    • Zhu, L., D. K. Henze, J. Bash, G. Jeong, K. Cady-Pereira, M. Shephard, M. Luo, F. Paulot, and S. Capps, Global evaluation of ammonia bi-directional exchange, Atmos. Chem. Phys. Discuss., 15, 4823-4877, doi:10.5194/acpd-15-4823-2015.
    • Jiang, Z., J. R. Worden, D. B. A. Jones, J.-T. Lin, W. Verstraeten, and D. K. Henze, Constraints on Asian ozone using Aura TES, OMI and Terra MOPITT, Atmos. Chem. Phys., 15, 99-112.
    • Lee, C.J., R.V. Martin, Henze D.K., Brauer M., Cohen A., and A. van Donkelaar, Sensitivity of global particulate-matter-related mortality to local precursor emissions, Environ. Sci. Technol., 49(7), 4335–4344, doi:10.1021/acs.est.5b00873, 2015.
    • Bousserez, N., D. K. Henze, A. Perkins, K. W. Bowman, M.Lee, J.Liu, D.B.A. Jones, F. Deng, Improved analysis-error covariance matrix for high-dimensional variational inversions: application to source estimation using a 3D atmospheric transport model. Q.J.R. Meteorol. Soc.. doi: 10.1002/qj.2495
  • 2014
    • Jiang, Z., D. B. A Jones, H. M. Worden, and D. K. Henze, Sensitivity of inferred regional CO source estimates to the vertical structure in CO as observed by MOPITT, Atmos. Chem. Phys. Discuss., 14, 22939-22984
    • Zhu, Q., Q. Zhuang, D. K. Henze, K. Bowman, M. Chen, Y. Liu, Y. He, H. Matsueda, T. Machida, and Y. Sawa, Constraining terrestrial ecosystem CO2 fluxes by integrating models of biogeochemistry and atmospheric transport and data of surface carbon fluxes and atmospheric CO2 concentrations, Atmos. Chem. Phys. Discuss., 14, 22587-22638
    • Mao, Y. H., Q. B. Li, D. K. Henze, Z. Jiang, D. B. A. Jones, M. Kopacz, C. He, L. Qi, M. Gao, W.-M. Hao, and K.-N. Liou, Variational estimates of black carbon emissions in the western United States, Atmos. Chem. Phys. Discuss., 14, 21865-21916
    • Liu, J., Bowman, K., Lee, M., Henze, D., Bousserez, N., Brix, H., Collatz, G., Menemenlis, D., Ott, L., Pawson, S., Jones, D., Nassar, R.. Carbon monitoring system flux estimation and attribution: impact of ACOS-GOSAT XCO2 sampling on the inference of terrestrial biospheric sources and sinks. Tellus B, North America, 66, may. 2014. Available at: http://www.tellusb.net/index.php/tellusb/article/view/22486
    • Lee, H., D. K. Henze, B. Alexander, and L. T., Murray, Investigating the sensitivity of surface-level nitrate seasonality in Antarctica to primary sources using a global model, Atmos. Environ., 89, 757--767, doi:0.1016/j.atmosenv.2014.03.003
    • Paulot, F., D. J. Jacob, R. W. Pinder, J. O. Bash, K. Travis, D. K. Henze, Ammonia emissions in the United States, Europe, and China derived by high-resolution inversion of ammonium wet deposition data: Interpretation with a new agricultural emissions inventory (MASAGE_NH3), J. Geophys. Res., 119, 7, 4343--4364, doi:10.1002/2013JD021130.
    • Lapina, K., D. K. Henze, J. B. Milford, M. Huang, M. Lin, A. M. Fiore, G. Carmichael, G. G. Pfister, and K. W. Bowman, Assessment of source contributions to seasonal vegetative exposure to ozone in the U.S., J. Geophys. Res., 119, 324-340, doi:10.1002/2013JD020905
    • Shen, Z., J. Liu, L. W. Horowitz, D. K. Henze, S. Fan, H. Levy II, D. L. Mauzerall, J. Lin, and S. Tao,.: Analysis of transpacific transport of black carbon during HIPPO-3: implications for black carbon aging, Atmos. Chem. Phys. Discuss., 14, 505-540, doi:10.5194/acpd-14-505-2014
    • Wells, K. C., D. B. Millet, K. E. Cady-Pereira, M. W. Shephard, D. K. Henze, N. Bousserez, E. C. Apel, J. de Gouw, C. Warneke, H. B. Singh, Quantifying global terrestrial methanol emissions using observations from the TES satellite sensor, Atmos. Chem. Phys., 14, 2555-2570
  • 2013
    • Walker, T. W., D. B. A. Jones, D. K. Henze, Z. Jiang, M. Parrington, F. Paulot, and Y. Rochon, Adjoint sensitivity analysis of North American surface ozone concentrations: Implications for dry deposition, American Geophysical Union, Fall Meeting 2013, abstract id. A33L-03.
    • Deng, F., D. B. A. Jones, D. K. Henze, N. Bousserez, K. W. Bowman, J. B. Fisher, R. Nassar, C. O'Dell, D. Wunch, P. O. Wennberg, E. A. Kort, S. C. Wofsy, T. Blumenstock, N. M. Deutscher, D. Griffith, F. Hase, P. Heikkinen, V. Sherlock, K. Strong, R. Sussmann, and T. Warneke, Inferring regional sources and sinks of atmospheric CO2 from GOSAT XCO2 data, Atmos. Chem. Phys. Discuss., 13, 26327-26388
    • Meland, B., X. Xu, D. K. Henze, J. Wang, Assessing remote polarimetric measurements sensitivities to aerosol emissions using the GEOS-Chem adjoint model, Atmos. Meas. Tech. Discuss., 6, 5447-5493, doi:10.5194/amtd-6-5447-2013
    • Xu, X., J. Wang, D. K. Henze, W. Qu, M. Kopacz (2013), Constraints on Aerosol Sources Using GEOS-Chem Adjoint and MODIS Radiances, and Evaluation with Multi-sensor (OMI, MISR) data, J. Geophys. Res., 118, doi:10.1002/jgrd.50515.
    • Paulot, F., D. J. Jacob and D. K. Henze, Sources and processes contributing to nitrogen deposition in biodiversity hotspots worldwide, Environ. Sci. Technol, 47, 3226-3233, doi:10.1021/es3027727.
    • Koo, J., Q. Wang, D. K. Henze, I. A. Waitz, S.R.H. Barrett, Spatial sensitivities of human health risk to intercontinental and high-altitude pollution, Atmos. Environ., 71, 140-147.
    • Kharol, S., R. V. Martin, S. Philip, S. Vogel, D. K. Henze, D. Chen, Y. Wang, Q. Zhang, C. L. Heald, Persistent Sensitivity of Asian Aerosol to Emissions of Nitrogen Oxides, Geophys. Res. Lett., 40, 1021-1026, doi:10.1002/grl.50234.
    • Jiang, Z., D. B. A. Jones, H. M. Worden, M. N. Deeter, D. K. Henze, J. Worden, and K. W. Bowman, Quantifying the impact of model biases in convective transport on inferred CO source estimates using multi-spectral CO retrievals from MOPITT, J. Geophys. Res.,118, doi:10.1029/jgrd.50216
    • L. Zhu, D. K. Henze, K. E. Cady-Pereira, M. W. Shephard, M. Luo, R. W. Pinder, J. O. Bash, G. Jeong, Constraining U.S. ammonia emissions using TES remote sensing observations and the GEOS-Chem adjoint model, J. Geophys. Res., 118, doi:10.1002/jgrd.50166
    • Koo, J., Q. Wang, D. K. Henze, I. A. Waitz, S.R.H. Barrett, Spatial sensitivities of human health risk to intercontinental and high-altitude pollution, Atmos. Environ., 71, 140-147
  • 2012
    • Bowman, K. W., and D. K. Henze, Attribution of direct ozone radiative forcing to spatially-resolved emissions, Geophys. Res. Lett., 39, L22704, doi:10.1029/2012GL053274.
    • Henze, D. K., D. T. Shindell, F. Akhtar, R. J. D. Spurr, R. W. Pinder, D. Loughlin, M. Kopacz, K. Singh, and C. Shim, Spatially refined aerosol direct radiative forcing efficiencies, Environ. Sci. Technol., 46, 9511 - 9518, dx.doi.org/10.1021/es301993s.
    • Karydis, V. A., S. L. Capps, R. H. Moore, A. Russell, D. K. Henze, and A. Nenes, Using a global aerosol model adjoint to unravel the footprint of spatially-distributed emissions on cloud droplet number and cloud albedo, Geophys. Res. Lett., 39, L24804, doi:10.1029/2012GL053346.
    • Parrington, M., P. I. Palmer, D. K. Henze, D. W. Tarasick, E. J. Hyer, R. C. Owen, C. Clerbaux, K. W. Bowman, M. N. Deeter, E. M. Barratt, P.-F. Coheur, D. Hurtmans, M. George, and J. R. Worden, The influence of boreal biomass burning emissions on the distribution of tropospheric ozone over North America and the North Atlantic during 2010, Atmos. Chem. Phys., 12, 2077-2098.
    • Paulot, F., D. K. Henze, and P. O. Wennberg, Impact of the isoprene photochemical cascade on tropical ozone, Atmos. Chem. Phys., 12, 1307-1325.
    • Singh, K. and A. Sandu, 2012: Variational chemical data assimilation with approximate adjoints. Computers and Geosciences, 40, 10-18.
    • Turner, A., D. K. Henze, R. V. Martin, and A. Hakami, The spatial extent of source influences on modeled column concentrations of short-lived species, Geophys. Res. Lett., 39, L12806, doi:10.1029/2012GL051832.
    • Walker, T., D. B. A. Jones, M. Parrington, D. K. Henze, L. T. Murray, J. W. Bottenheim, K. Anlauf, J. R. Worden, K. W. Bowman, C. Shim, K. Singh, M. Kopacz, D. W. Tarasick, J. Davies, P. von der Gathen, and C. C. Carouge, Impacts of midlatitude precursor emissions and local photochemistry on ozone abundances in the Arctic, J. Geophys. Res.,117, D01305 doi:10.1029/2011JD016370.
    • Wang, J., X. Xu, D. K. Henze, Q. Ji, S.-C. Tsay (2012), J. Huang, Top-Down Estimate of Dust Emissions through Integration of MODIS and MISR Aerosol Retrievals with the GEOS-Chem adjoint model, Geophys. Res. Lett., 39, L08802.
    • Wecht, K. J., D. J. Jacob, S. C. Wofsy, E. A. Kort, J. R. Worden, S. S. Kulawik, D. K. Henze, M. Kopacz, and V. H. Payne, Validation of TES methane with HIPPO aircraft observations: implications for inverse modeling of methane sources, Atmos. Chem. Phys., 12, 1823-1832.
    • Singh, K. and A. Sandu (2012). "Variational chemical data assimilation with approximate adjoints." Computers and Geosciences 40: 10-18.
  • 2011
    • Jiang, Z., D. B. A. Jones, M. Kopacz, J. Liu, D. K. Henze, and C. Heald, Quantifying the impact of model errors on top-down estimates of carbon monoxide emissions using satellite observations, J. Geophys. Res., 116, D15306, doi:10.1029/2010JD015282.
    • Jiang, Z., D. B. A. Jones, M. Kopacz, J. Liu, D. K. Henze, and C. Heald (2011), Quantifying the impact of model errors on top-down estimates of carbon monoxide emissions using satellite observations, J. Geophys. Res., 116, D15306, doi:10.1029/2010JD015282.
    • 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., 11, 2837-2852.
  • 2010
    • 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), Atoms. Chem. Phys., 10, 855-876.
    • 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.
    • Parrington, M., P. I. Palmer, D. K. Henze, D. W. Tarasick, E. J. Hyer, R. C. Owen, C. Clerbaux, K. W. Bowman, M. N. Deeter, E. M. Barratt, P.-F. Coheur, D. Hurtmans, M. George, and J. R. Worden (2012), The influence of boreal biomass burning emissions on the distribution of tropospheric ozone over North America and the North Atlantic during 2010, Atmos. Chem. Phys., 12, 2077-2098
    • Singh, K., Jardak, M., Sandu, A., Bowman, K., Lee, M., and Jones, D. (2010): 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. http://www.geosci-model-dev-discuss.net/3/1783/2010/gmdd-3-1783-2010.html
  • 2009
    • Eller, P., K. Singh, A. Sandu, K. Bowman, D. K. Henze, and M. Lee (2009), Implementation and evaluation of an array of chemical solvers in a global chemical transport model, Geosci. Mod. Devel., 2, 185-207.
    • 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, Atoms. Chem. Phys., 9, 5877-5903.
    • 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., 114, D04305, doi:10.1029/2007JD009264.
    • Pye, H. O. T., H. Liao, S. Wu, L. J. Mickely, D. J. Jacob, D. K. Henze, and J. H. Seinfeld (2009), Effect of changes in climate and emissions on future sulfate-nitrate-ammonium aerosol levels in the United States, J. Geophys. Res., 114, D01205, doi:10.1029/2008JD010701.
    • 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.
  • 2007
    • 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

  • 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
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