https://wiki.seas.harvard.edu/geos-chem/api.php?action=feedcontributions&user=Alex+Turner&feedformat=atomGeos-chem - User contributions [en]2024-03-29T14:59:29ZUser contributionsMediaWiki 1.24.2https://wiki.seas.harvard.edu/geos-chem/index.php?title=CH4_simulation&diff=19234CH4 simulation2015-02-24T17:17:39Z<p>Alex Turner: /* References */</p>
<hr />
<div>This page contains information about the methane (CH4) simulation in GEOS-Chem.<br />
<br />
== Overview ==<br />
<br />
=== Authors and collaborators ===<br />
* [mailto:maasakkers@fas.harvard.edu Bram Maasakkers] ''(Harvard)''<br />
* Alex Turner ''(Harvard; aturner [at] fas [dot] harvard [dot] edu)''<br />
* Kevin Wecht ''(formerly @ Harvard)''<br />
* Christopher Pickett-Heaps ''(formerly @ Harvard)''<br />
* Jerome Drevet ''(formerly @ EPFL)''<br />
* James Wang ''(formerly @ Harvard)''<br />
<br />
=== CH4 simulation user groups ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group<br />
!Personnel<br />
!Projects<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/ Harvard University]<br />
|[mailto:maasakkers@fas.harvard.edu Bram Maasakkers]<br>[mailto:jsheng@seas.harvard.edu Jianxiong Sheng]<br>Alex Turner<br />
|North American methane sources;<br>International oil and gas emissions;<br>SCIAMACHY, GOSAT, & TROPOMI<br />
|-valign="top"<br />
<br />
|}<br />
<br />
=== Notes about the methane simulation ===<br />
<br />
:1. '''annual_met.pro:''' The methane simulation uses monthly and annual average skin temperature and soil moisture values from the met fields. These are calculated offline using IDL ("annual_met.pro"). This file can be found on the ftp site in the methane data directory with the LPJ wetland emission scheme (e.g., "GEOS_0.5x0.666_NA/CH4_201305/wetlands"). The script should work as is for 2004-2011, however we don't currently have the met data for 2012 so you may need to modify "global_ch4_mod.F" if you're interested in 2012 or 2013.<br />
::: '''Subroutine "WETLAND_EMIS"<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
::: '''Subroutine "RICE_EMIS"<br />
! Get annual and monthly mean soil wetness from GEOS<br />
! One file contains both monthly and annual mean GWETTOP<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
:2. '''Seasonality of Rice Emissions:''' Seasonality in the rice emissions is imposed through annual and monthly average soil moisture values. This works reasonably well for major rice growing areas like South/East Asia where rice paddies are rain-fed, but it fails in other regions. For example, California rice paddies are irrigated and crops are grown in the summer, precisely when the natural soil is the driest. You can enter the "global_ch4_mod.F", subroutine "RICE_EMIS", and impose any seasonality you want on the annual emission rates from EDGAR.<br />
<br />
:3. '''Potential Global Mean Bias:''' The methane simulation may not simulate global average concentrations accurately. That is, you may have a mean bias of up to +/-30ppbv when you compare the simulation to observations. A global mean bias means that the model has a slight imbalance between the sources and sinks relative to the world. You may want to consider removing this mean bias before analyzing your model concentrations.<br />
<br />
--[[User:Alex Turner|Alex Turner]] 11:01, 24 January 2014 (EST)<br />
<br />
== Recent science updates ==<br />
<br />
The following updates were recently added into the GEOS-Chem CH4 simulation:<br />
<br />
=== Update CH4 emissions to EDGAR v4.2 ===<br />
<br />
The CH4 simulation now uses emissions from the EDGAR v4.2 inventory.<br />
<br />
==== In GEOS-Chem v10-01 and newer versions ====<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, EDGAR v4.2 CH4 emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CH4/v2014-09/README new emission data files for the CH4 simulation] (in [http://ferret.wrc.noaa.gov/noaa_coop/coop_cdf_profile.html COARDS-compliant netCDF format]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 12:17, 17 February 2015 (EST)<br />
<br />
==== In GEOS-Chem versions prior to v10-01 ====<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02m|v9-02m]] and approved on 30 Jul 2013.'''''<br />
'''''This update is included in Adjoint [[GEOS-Chem_Adjoint_v35 | v35d]].'''''<br />
<br />
Kevin Wecht has prepared EDGAR v4.2 emissions of methane for 2004-2008. The data files are available at:<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/CH4_201305/<br />
<br />
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.<br />
<br />
Modifications to subroutines <tt>RICE_EMIS</tt> and <tt>ASEASONAL_ANTHRO_EMIS</tt> in <tt>global_ch4_mod.F</tt> include changing the directory names and updating CYEAR and XTAU as follows:<br />
<br />
WRITE( CYEAR, '(i4)' ) GET_YEAR()<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
<br />
IF ( GET_YEAR() .LT. 2004 ) THEN<br />
CYEAR='2004'<br />
XTAU = GET_TAU0( 1, 1, 2004 )<br />
ENDIF<br />
IF ( GET_YEAR() .GT. 2008 ) THEN<br />
CYEAR='2008'<br />
XTAU = GET_TAU0( 1, 1, 2008 )<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:53, 2 July 2013 (EDT)<br />
<br />
=== Update methane emissions and add capability for North America nested grid ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
'''''Kevin Wecht wrote:'''''<br />
<br />
:I have some GEOS-Chem methane updates that I'd like to add to the standard code. <br />
<br />
:#GFED emissions - I've updated GFED-2 and GFED-3 biomass burning to include methane emissions.<br />
:#Methane simulation - I've updated emissions and error catches to make the simulation compatible with the nested simulation over North America. I added linearized CH4 chemistry from GMI output (CH4 loss frequencies generated by Lee Murray). These changes should be made to the data directory:<br />
<br />
:::a. Replace Carbon_soil, Carbon_litter, and Wetfrac files in data directory (for all horizontal resolutions)<br />
:::b. Add 2010-2011 TSKIN and GWETTOP files to data directory (for all horizontal resolutions)<br />
:::c. Add nested north american OH files to OH directory<br />
:::d. Add biofuel emissions to data directory (for all horizontal resolutions)<br />
:::e. Add all emission files to data directory for nested North America simulation<br />
<br />
The [[CH4_simulation#Error_reading_GWETTOP_fields|error in reading GWETTOP fields]] is also fixed in this update.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:35, 2 February 2012 (EST)<br />
<br />
== Validation ==<br />
<br />
TBD<br />
<br />
== References ==<br />
<br />
#Turner, A. J., Jacob, D. J., Wecht, K. J., Maasakkers, J. D., Biraud, S. C., Boesch, H., Bowman, K. W., Deutscher, N. M., Dubey, M. K., Griffith, D. W. T., Hase, F., Kuze, A., Notholt, J., Ohyama, H., Parker, R., Payne, V. H., Sussmann, R., Velazco, V. A., Warneke, T., Wennberg, P. O., and Wunch, D.: ''Estimating global and North American methane emissions with high spatial resolution using GOSAT satellite data'', <u>Atmos. Chem. Phys. Discuss.</u>, 15, 4495-4536, doi:10.5194/acpd-15-4495-2015, 2015.<br />
#Turner, A. J. and Jacob, D. J.: ''Balancing aggregation and smoothing errors in inverse models'', <u>Atmos. Chem. Phys. Discuss.</u>, 15, 1001-1026, doi:10.5194/acpd-15-1001-2015, 2015.<br />
#Wecht, K.J., D.J. Jacob, C. Frankenberg, Z. Jiang, and D.R. Blake, ''Mapping of North America methane emissions with high spatial resolution by inversion of SCIAMACHY satellite data'', submitted to <u>J. Geophys. Res.</u>, 2014.<br />
#Wecht, K.J., D.J. Jacob, M.P. Sulprizio, G.W. Santoni, S.C. Wofsy, R. Parker, H. Bösch, and J.R. Worden, ''Spatially resolving methane emissions in California: constraints from the CalNex aircraft campaign and from present (GOSAT, TES) and future (TROPOMI, geostationary) satellite observations'', <u>Atm. Chem. Phys. Discuss.</u>, '''14''', 4119-4198, doi:10.5194/acpd-14-4119-2014, 2014.<br />
#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'', <u>Atmos. Chem. Phys.</u>, '''12''', 1823-1832, 2012.<br />
#Pickett-Heaps, C.A., D.J. Jacob, K.J. Wecht, E.A. Kort, S.C. Wofsy, G.S. Diskin, D.E.J. Worthy, J.O. Kaplan, I. Bey, and J. Drevet, ''Magnitude of seasonality of wetland methane emissions from the Hudson Bay Lowlands (Canada)'', <u>Atmos. Chem. Phys.</u>, '''11(8)''', 3773-3779, doi:10.5194/acp-11-3773-2011, 2011.<br />
#Wang, J.S., J.A. Logan, M.B. McElroy, B.N. Duncan, I.A. Megretskaia, and R.M. Yantosca, ''A 3-D model analysis of the slowdown and interannual variability in the methane growth rate from 1988 to 1997'', <u>Global Biogeochem. Cycles</u>, '''18''', GB3011, doi:10.1029/2003GB002180, 2004.<br />
<br />
--[[User:Alex Turner|Alex Turner]] 12:17, 24 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved ==<br />
<br />
The following bugs and/or issues with the code have now been resolved:<br />
<br />
=== Now call INIT_GLOBAL_CH4 from input_mod.F ===<br />
<br />
'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''<br />
<br />
Prior to [[GEOS-Chem v10-01]], routine <tt>INIT_GLOBAL_CH4</tt> (in module <tt>GeosCore/global_ch4_mod.F</tt>) was called from the main driver routine <tt>main.F</tt> at the start of the simulation. <br />
<br />
In order to make the code more compatible with our [[Grid-Independent GEOS-Chem]] development, we now call <tt>INIT_TAGGED_CH4</tt> from routine <tt>GIGC_INIT_EXTRA</tt> (in module <tt>GeosCore/input_mod.F</tt>).<br />
<br />
--[[User:Bmy|Bob Y.]] 16:59, 30 May 2014 (EDT)<br />
<br />
=== Minor fixes to CH4 simulation for MERRA meteorology ===<br />
<br />
'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''<br />
<br />
We have made a couple of fixes to the CH4 simulation module (<tt>GeosCore/global_ch4_mod.F</tt>) for compatibility with the [[MERRA]] met fields. At lines 1114, and again at line 1503, there were #if blocks that looked like this:<br />
<br />
#if defined( GEOS_5 ) || defined( GEOS_FP )<br />
<br />
but these should have been:<br />
<br />
#if defined( GEOS_5 ) || defined( GEOS_FP ) || defined( MERRA )<br />
<br />
Furthermore, in data directory <tt>GEOS_4x5/CH4_201305/wetlands</tt>, we have symbolically linked files:<br />
<br />
GWETTOP.geos5.4x5.YYYY.bpch --> GWETTOP.merra.4x5.YYYY.bpch<br />
TSKIN.geos5.4x5.YYYY.bpch --> TSKIN.merra.4x5.YYYY.bpch<br />
<br />
where <tt>YYYY = { 2004, 2005, 2006, 2007, 2008, 2009, 2010 }</tt>.<br />
<br />
These issues were discovered with the [[GEOS-Chem Unit Tester]].<br />
<br />
--[[User:Bmy|Bob Y.]] 16:59, 30 May 2014 (EDT)<br />
<br />
=== Fixes for wetland emissions ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''These issues were resolved during the [[GEOS-Chem_v9-02#Period_of_public_comment|public comment period]] following the provisional release of GEOS-Chem v9-02 and were included in the official release of [[GEOS-Chem v9-02]] (03 Mar 2014).'''''<br />
<br />
'''''Kevin Wecht''''' wrote:<br />
<br />
:I have some updates/bug fixes to wetland emissions in the methane simulation. Both changes impact global_ch4_mod.F, subroutine WETLAND_EMIS.<br />
<br />
::1. Christopher Pickett-Heaps added a feature that zeroes wetland emissions if snow covers the ground. This was never incorporated into the standard code. It is included in the attached file.<br />
<br />
::2. Parameters in the subroutine are not correct. The following values are the correct and are included in the attached file:<br />
MOIST_SCALE = 0.205<br />
EMIT_FACT = 0.018<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 16:11, 23 January 2014 (EST)<br><br />
--[[User:Bmy|Bob Y.]] 10:25, 4 April 2014 (EDT)<br />
<br />
=== Error reading GWETTOP fields ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
There is a file read error in the current CH4 simulation. We will fix this issue in [[GEOS-Chem v9-01-03]].<br />
<br />
In RICE_EMIS (global_ch4_mod.F), XTAU is reset to the wrong value when GEWTTOP is read. Kevin Wecht provided a fix that accounts for different availabilities of GEOS-4 and GEOS-5 met fields. Prior to setting FILENAME for GWETTOP , add the following:<br />
<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2009 ) YEAR = 2009<br />
#elif defined( GEOS_4 )<br />
IF ( YEAR .LT. 2000 ) YEAR = 2000<br />
IF ( YEAR .GT. 2006 ) YEAR = 2006<br />
#endif<br />
WRITE( CYEAR, '(i4)' ) YEAR<br />
<br />
:Also change:<br />
<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, GET_YEAR() )<br />
<br />
:to:<br />
<br />
XTAU = GET_TAU0( 1, 1, YEAR )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, YEAR )<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 18:06, 2 February 2012 (EST)<br />
<br />
== Unresolved issues ==<br />
<br />
None reported so far.<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 30 March 2012 (EDT)</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=CH4_simulation&diff=19233CH4 simulation2015-02-24T17:15:53Z<p>Alex Turner: /* References */</p>
<hr />
<div>This page contains information about the methane (CH4) simulation in GEOS-Chem.<br />
<br />
== Overview ==<br />
<br />
=== Authors and collaborators ===<br />
* [mailto:maasakkers@fas.harvard.edu Bram Maasakkers] ''(Harvard)''<br />
* Alex Turner ''(Harvard; aturner [at] fas [dot] harvard [dot] edu)''<br />
* Kevin Wecht ''(formerly @ Harvard)''<br />
* Christopher Pickett-Heaps ''(formerly @ Harvard)''<br />
* Jerome Drevet ''(formerly @ EPFL)''<br />
* James Wang ''(formerly @ Harvard)''<br />
<br />
=== CH4 simulation user groups ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group<br />
!Personnel<br />
!Projects<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/ Harvard University]<br />
|[mailto:maasakkers@fas.harvard.edu Bram Maasakkers]<br>[mailto:jsheng@seas.harvard.edu Jianxiong Sheng]<br>Alex Turner<br />
|North American methane sources;<br>International oil and gas emissions;<br>SCIAMACHY, GOSAT, & TROPOMI<br />
|-valign="top"<br />
<br />
|}<br />
<br />
=== Notes about the methane simulation ===<br />
<br />
:1. '''annual_met.pro:''' The methane simulation uses monthly and annual average skin temperature and soil moisture values from the met fields. These are calculated offline using IDL ("annual_met.pro"). This file can be found on the ftp site in the methane data directory with the LPJ wetland emission scheme (e.g., "GEOS_0.5x0.666_NA/CH4_201305/wetlands"). The script should work as is for 2004-2011, however we don't currently have the met data for 2012 so you may need to modify "global_ch4_mod.F" if you're interested in 2012 or 2013.<br />
::: '''Subroutine "WETLAND_EMIS"<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
::: '''Subroutine "RICE_EMIS"<br />
! Get annual and monthly mean soil wetness from GEOS<br />
! One file contains both monthly and annual mean GWETTOP<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
:2. '''Seasonality of Rice Emissions:''' Seasonality in the rice emissions is imposed through annual and monthly average soil moisture values. This works reasonably well for major rice growing areas like South/East Asia where rice paddies are rain-fed, but it fails in other regions. For example, California rice paddies are irrigated and crops are grown in the summer, precisely when the natural soil is the driest. You can enter the "global_ch4_mod.F", subroutine "RICE_EMIS", and impose any seasonality you want on the annual emission rates from EDGAR.<br />
<br />
:3. '''Potential Global Mean Bias:''' The methane simulation may not simulate global average concentrations accurately. That is, you may have a mean bias of up to +/-30ppbv when you compare the simulation to observations. A global mean bias means that the model has a slight imbalance between the sources and sinks relative to the world. You may want to consider removing this mean bias before analyzing your model concentrations.<br />
<br />
--[[User:Alex Turner|Alex Turner]] 11:01, 24 January 2014 (EST)<br />
<br />
== Recent science updates ==<br />
<br />
The following updates were recently added into the GEOS-Chem CH4 simulation:<br />
<br />
=== Update CH4 emissions to EDGAR v4.2 ===<br />
<br />
The CH4 simulation now uses emissions from the EDGAR v4.2 inventory.<br />
<br />
==== In GEOS-Chem v10-01 and newer versions ====<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, EDGAR v4.2 CH4 emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CH4/v2014-09/README new emission data files for the CH4 simulation] (in [http://ferret.wrc.noaa.gov/noaa_coop/coop_cdf_profile.html COARDS-compliant netCDF format]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 12:17, 17 February 2015 (EST)<br />
<br />
==== In GEOS-Chem versions prior to v10-01 ====<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02m|v9-02m]] and approved on 30 Jul 2013.'''''<br />
'''''This update is included in Adjoint [[GEOS-Chem_Adjoint_v35 | v35d]].'''''<br />
<br />
Kevin Wecht has prepared EDGAR v4.2 emissions of methane for 2004-2008. The data files are available at:<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/CH4_201305/<br />
<br />
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.<br />
<br />
Modifications to subroutines <tt>RICE_EMIS</tt> and <tt>ASEASONAL_ANTHRO_EMIS</tt> in <tt>global_ch4_mod.F</tt> include changing the directory names and updating CYEAR and XTAU as follows:<br />
<br />
WRITE( CYEAR, '(i4)' ) GET_YEAR()<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
<br />
IF ( GET_YEAR() .LT. 2004 ) THEN<br />
CYEAR='2004'<br />
XTAU = GET_TAU0( 1, 1, 2004 )<br />
ENDIF<br />
IF ( GET_YEAR() .GT. 2008 ) THEN<br />
CYEAR='2008'<br />
XTAU = GET_TAU0( 1, 1, 2008 )<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:53, 2 July 2013 (EDT)<br />
<br />
=== Update methane emissions and add capability for North America nested grid ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
'''''Kevin Wecht wrote:'''''<br />
<br />
:I have some GEOS-Chem methane updates that I'd like to add to the standard code. <br />
<br />
:#GFED emissions - I've updated GFED-2 and GFED-3 biomass burning to include methane emissions.<br />
:#Methane simulation - I've updated emissions and error catches to make the simulation compatible with the nested simulation over North America. I added linearized CH4 chemistry from GMI output (CH4 loss frequencies generated by Lee Murray). These changes should be made to the data directory:<br />
<br />
:::a. Replace Carbon_soil, Carbon_litter, and Wetfrac files in data directory (for all horizontal resolutions)<br />
:::b. Add 2010-2011 TSKIN and GWETTOP files to data directory (for all horizontal resolutions)<br />
:::c. Add nested north american OH files to OH directory<br />
:::d. Add biofuel emissions to data directory (for all horizontal resolutions)<br />
:::e. Add all emission files to data directory for nested North America simulation<br />
<br />
The [[CH4_simulation#Error_reading_GWETTOP_fields|error in reading GWETTOP fields]] is also fixed in this update.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:35, 2 February 2012 (EST)<br />
<br />
== Validation ==<br />
<br />
TBD<br />
<br />
== References ==<br />
<br />
#Turner, A. J., Jacob, D. J., Wecht, K. J., Maasakkers, J. D., Biraud, S. C., Boesch, H., Bowman, K. W., Deutscher, N. M., Dubey, M. K., Griffith, D. W. T., Hase, F., Kuze, A., Notholt, J., Ohyama, H., Parker, R., Payne, V. H., Sussmann, R., Velazco, V. A., Warneke, T., Wennberg, P. O., and Wunch, D.: ''Estimating global and North American methane emissions with high spatial resolution using GOSAT satellite data'', <u>Atmos. Chem. Phys. Discuss.</u>, 15, 4495-4536, doi:10.5194/acpd-15-4495-2015, 2015.<br />
#Turner, A. J. and Jacob, D. J.: ''Balancing aggregation and smoothing errors in inverse models'', <u>Atmos. Chem. Phys. Discuss.</u>, 15, 1001-1026, doi:10.5194/acpd-15-1001-2015, 2015.<br />
#Wecht, K.J., D.J. Jacob, C. Frankenberg, Z. Jiang, and D.R. Blake, ''Mapping of North America methane emissions with high spatial resolution by inversion of SCIAMACHY satellite data'', submitted to <u>J. Geophys. Res.</u>, 2014.<br />
#Wecht, K.J., D.J. Jacob, M.P. Sulprizio, G.W. Santoni, S.C. Wofsy, R. Parker, H. Bösch, and J.R. Worden, ''Spatially resolving methane emissions in California: constraints from the CalNex aircraft campaign and from present (GOSAT, TES) and future (TROPOMI, geostationary) satellite observations'', <u>Atm. Chem. Phys. Discuss.</u>, '''14''', 4119-4198, doi:10.5194/acpd-14-4119-2014, 2014.<br />
#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'', <u>Atmos. Chem. Phys.</u>, '''12''', 1823-1832, 2012.<br />
#Pickett-Heaps, C.A., D.J. Jacob, K.J. Wecht, E.A. Kort, S.C. Wofsy, G.S. Diskin, D.E.J. Worthy, J.O. Kaplan, I. Bey, and J. Drevet, ''Magnitude of seasonality of wetland methane emissions from the Hudson Bay Lowlands (Canada)'', <u>Atmos. Chem. Phys.</u>, '''11(8)''', 3773-3779, doi:10.5194/acp-11-3773-2011, 2011.<br />
#Wang, J.S., J.A. Logan, M.B. McElroy, B.N. Duncan, I.A. Megretskaia, and R.M. Yantosca, ''A 3-D model analysis of the slowdown and interannual variability in the methane growth rate from 1988 to 1997'', <u>Global Biogeochem. Cycles</u>, '''18''', GB3011, doi:10.1029/2003GB002180, 2004.<br />
<br />
--[[User:Bmy|Bob Y.]] 15:45, 9 April 2014 (EDT)<br />
<br />
== Previous issues that are now resolved ==<br />
<br />
The following bugs and/or issues with the code have now been resolved:<br />
<br />
=== Now call INIT_GLOBAL_CH4 from input_mod.F ===<br />
<br />
'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''<br />
<br />
Prior to [[GEOS-Chem v10-01]], routine <tt>INIT_GLOBAL_CH4</tt> (in module <tt>GeosCore/global_ch4_mod.F</tt>) was called from the main driver routine <tt>main.F</tt> at the start of the simulation. <br />
<br />
In order to make the code more compatible with our [[Grid-Independent GEOS-Chem]] development, we now call <tt>INIT_TAGGED_CH4</tt> from routine <tt>GIGC_INIT_EXTRA</tt> (in module <tt>GeosCore/input_mod.F</tt>).<br />
<br />
--[[User:Bmy|Bob Y.]] 16:59, 30 May 2014 (EDT)<br />
<br />
=== Minor fixes to CH4 simulation for MERRA meteorology ===<br />
<br />
'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''<br />
<br />
We have made a couple of fixes to the CH4 simulation module (<tt>GeosCore/global_ch4_mod.F</tt>) for compatibility with the [[MERRA]] met fields. At lines 1114, and again at line 1503, there were #if blocks that looked like this:<br />
<br />
#if defined( GEOS_5 ) || defined( GEOS_FP )<br />
<br />
but these should have been:<br />
<br />
#if defined( GEOS_5 ) || defined( GEOS_FP ) || defined( MERRA )<br />
<br />
Furthermore, in data directory <tt>GEOS_4x5/CH4_201305/wetlands</tt>, we have symbolically linked files:<br />
<br />
GWETTOP.geos5.4x5.YYYY.bpch --> GWETTOP.merra.4x5.YYYY.bpch<br />
TSKIN.geos5.4x5.YYYY.bpch --> TSKIN.merra.4x5.YYYY.bpch<br />
<br />
where <tt>YYYY = { 2004, 2005, 2006, 2007, 2008, 2009, 2010 }</tt>.<br />
<br />
These issues were discovered with the [[GEOS-Chem Unit Tester]].<br />
<br />
--[[User:Bmy|Bob Y.]] 16:59, 30 May 2014 (EDT)<br />
<br />
=== Fixes for wetland emissions ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''These issues were resolved during the [[GEOS-Chem_v9-02#Period_of_public_comment|public comment period]] following the provisional release of GEOS-Chem v9-02 and were included in the official release of [[GEOS-Chem v9-02]] (03 Mar 2014).'''''<br />
<br />
'''''Kevin Wecht''''' wrote:<br />
<br />
:I have some updates/bug fixes to wetland emissions in the methane simulation. Both changes impact global_ch4_mod.F, subroutine WETLAND_EMIS.<br />
<br />
::1. Christopher Pickett-Heaps added a feature that zeroes wetland emissions if snow covers the ground. This was never incorporated into the standard code. It is included in the attached file.<br />
<br />
::2. Parameters in the subroutine are not correct. The following values are the correct and are included in the attached file:<br />
MOIST_SCALE = 0.205<br />
EMIT_FACT = 0.018<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 16:11, 23 January 2014 (EST)<br><br />
--[[User:Bmy|Bob Y.]] 10:25, 4 April 2014 (EDT)<br />
<br />
=== Error reading GWETTOP fields ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
There is a file read error in the current CH4 simulation. We will fix this issue in [[GEOS-Chem v9-01-03]].<br />
<br />
In RICE_EMIS (global_ch4_mod.F), XTAU is reset to the wrong value when GEWTTOP is read. Kevin Wecht provided a fix that accounts for different availabilities of GEOS-4 and GEOS-5 met fields. Prior to setting FILENAME for GWETTOP , add the following:<br />
<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2009 ) YEAR = 2009<br />
#elif defined( GEOS_4 )<br />
IF ( YEAR .LT. 2000 ) YEAR = 2000<br />
IF ( YEAR .GT. 2006 ) YEAR = 2006<br />
#endif<br />
WRITE( CYEAR, '(i4)' ) YEAR<br />
<br />
:Also change:<br />
<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, GET_YEAR() )<br />
<br />
:to:<br />
<br />
XTAU = GET_TAU0( 1, 1, YEAR )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, YEAR )<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 18:06, 2 February 2012 (EST)<br />
<br />
== Unresolved issues ==<br />
<br />
None reported so far.<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 30 March 2012 (EDT)</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=CH4_simulation&diff=19232CH4 simulation2015-02-24T17:11:50Z<p>Alex Turner: /* CH4 simulation user groups */</p>
<hr />
<div>This page contains information about the methane (CH4) simulation in GEOS-Chem.<br />
<br />
== Overview ==<br />
<br />
=== Authors and collaborators ===<br />
* [mailto:maasakkers@fas.harvard.edu Bram Maasakkers] ''(Harvard)''<br />
* Alex Turner ''(Harvard; aturner [at] fas [dot] harvard [dot] edu)''<br />
* Kevin Wecht ''(formerly @ Harvard)''<br />
* Christopher Pickett-Heaps ''(formerly @ Harvard)''<br />
* Jerome Drevet ''(formerly @ EPFL)''<br />
* James Wang ''(formerly @ Harvard)''<br />
<br />
=== CH4 simulation user groups ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group<br />
!Personnel<br />
!Projects<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/ Harvard University]<br />
|[mailto:maasakkers@fas.harvard.edu Bram Maasakkers]<br>[mailto:jsheng@seas.harvard.edu Jianxiong Sheng]<br>Alex Turner<br />
|North American methane sources;<br>International oil and gas emissions;<br>SCIAMACHY, GOSAT, & TROPOMI<br />
|-valign="top"<br />
<br />
|}<br />
<br />
=== Notes about the methane simulation ===<br />
<br />
:1. '''annual_met.pro:''' The methane simulation uses monthly and annual average skin temperature and soil moisture values from the met fields. These are calculated offline using IDL ("annual_met.pro"). This file can be found on the ftp site in the methane data directory with the LPJ wetland emission scheme (e.g., "GEOS_0.5x0.666_NA/CH4_201305/wetlands"). The script should work as is for 2004-2011, however we don't currently have the met data for 2012 so you may need to modify "global_ch4_mod.F" if you're interested in 2012 or 2013.<br />
::: '''Subroutine "WETLAND_EMIS"<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
::: '''Subroutine "RICE_EMIS"<br />
! Get annual and monthly mean soil wetness from GEOS<br />
! One file contains both monthly and annual mean GWETTOP<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
:2. '''Seasonality of Rice Emissions:''' Seasonality in the rice emissions is imposed through annual and monthly average soil moisture values. This works reasonably well for major rice growing areas like South/East Asia where rice paddies are rain-fed, but it fails in other regions. For example, California rice paddies are irrigated and crops are grown in the summer, precisely when the natural soil is the driest. You can enter the "global_ch4_mod.F", subroutine "RICE_EMIS", and impose any seasonality you want on the annual emission rates from EDGAR.<br />
<br />
:3. '''Potential Global Mean Bias:''' The methane simulation may not simulate global average concentrations accurately. That is, you may have a mean bias of up to +/-30ppbv when you compare the simulation to observations. A global mean bias means that the model has a slight imbalance between the sources and sinks relative to the world. You may want to consider removing this mean bias before analyzing your model concentrations.<br />
<br />
--[[User:Alex Turner|Alex Turner]] 11:01, 24 January 2014 (EST)<br />
<br />
== Recent science updates ==<br />
<br />
The following updates were recently added into the GEOS-Chem CH4 simulation:<br />
<br />
=== Update CH4 emissions to EDGAR v4.2 ===<br />
<br />
The CH4 simulation now uses emissions from the EDGAR v4.2 inventory.<br />
<br />
==== In GEOS-Chem v10-01 and newer versions ====<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, EDGAR v4.2 CH4 emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CH4/v2014-09/README new emission data files for the CH4 simulation] (in [http://ferret.wrc.noaa.gov/noaa_coop/coop_cdf_profile.html COARDS-compliant netCDF format]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 12:17, 17 February 2015 (EST)<br />
<br />
==== In GEOS-Chem versions prior to v10-01 ====<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02m|v9-02m]] and approved on 30 Jul 2013.'''''<br />
'''''This update is included in Adjoint [[GEOS-Chem_Adjoint_v35 | v35d]].'''''<br />
<br />
Kevin Wecht has prepared EDGAR v4.2 emissions of methane for 2004-2008. The data files are available at:<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/CH4_201305/<br />
<br />
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.<br />
<br />
Modifications to subroutines <tt>RICE_EMIS</tt> and <tt>ASEASONAL_ANTHRO_EMIS</tt> in <tt>global_ch4_mod.F</tt> include changing the directory names and updating CYEAR and XTAU as follows:<br />
<br />
WRITE( CYEAR, '(i4)' ) GET_YEAR()<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
<br />
IF ( GET_YEAR() .LT. 2004 ) THEN<br />
CYEAR='2004'<br />
XTAU = GET_TAU0( 1, 1, 2004 )<br />
ENDIF<br />
IF ( GET_YEAR() .GT. 2008 ) THEN<br />
CYEAR='2008'<br />
XTAU = GET_TAU0( 1, 1, 2008 )<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:53, 2 July 2013 (EDT)<br />
<br />
=== Update methane emissions and add capability for North America nested grid ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
'''''Kevin Wecht wrote:'''''<br />
<br />
:I have some GEOS-Chem methane updates that I'd like to add to the standard code. <br />
<br />
:#GFED emissions - I've updated GFED-2 and GFED-3 biomass burning to include methane emissions.<br />
:#Methane simulation - I've updated emissions and error catches to make the simulation compatible with the nested simulation over North America. I added linearized CH4 chemistry from GMI output (CH4 loss frequencies generated by Lee Murray). These changes should be made to the data directory:<br />
<br />
:::a. Replace Carbon_soil, Carbon_litter, and Wetfrac files in data directory (for all horizontal resolutions)<br />
:::b. Add 2010-2011 TSKIN and GWETTOP files to data directory (for all horizontal resolutions)<br />
:::c. Add nested north american OH files to OH directory<br />
:::d. Add biofuel emissions to data directory (for all horizontal resolutions)<br />
:::e. Add all emission files to data directory for nested North America simulation<br />
<br />
The [[CH4_simulation#Error_reading_GWETTOP_fields|error in reading GWETTOP fields]] is also fixed in this update.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:35, 2 February 2012 (EST)<br />
<br />
== Validation ==<br />
<br />
TBD<br />
<br />
== References ==<br />
<br />
#Wecht, K.J., D.J. Jacob, C. Frankenberg, Z. Jiang, and D.R. Blake, ''Mapping of North America methane emissions with high spatial resolution by inversion of SCIAMACHY satellite data'', submitted to <u>J. Geophys. Res.</u>, 2014.<br />
#Wecht, K.J., D.J. Jacob, M.P. Sulprizio, G.W. Santoni, S.C. Wofsy, R. Parker, H. Bösch, and J.R. Worden, ''Spatially resolving methane emissions in California: constraints from the CalNex aircraft campaign and from present (GOSAT, TES) and future (TROPOMI, geostationary) satellite observations'', <u>Atm. Chem. Phys. Discuss.</u>, '''14''', 4119-4198, doi:10.5194/acpd-14-4119-2014, 2014.<br />
#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'', <u>Atmos. Chem. Phys.</u>, '''12''', 1823-1832, 2012.<br />
#Pickett-Heaps, C.A., D.J. Jacob, K.J. Wecht, E.A. Kort, S.C. Wofsy, G.S. Diskin, D.E.J. Worthy, J.O. Kaplan, I. Bey, and J. Drevet, ''Magnitude of seasonality of wetland methane emissions from the Hudson Bay Lowlands (Canada)'', <u>Atmos. Chem. Phys.</u>, '''11(8)''', 3773-3779, doi:10.5194/acp-11-3773-2011, 2011.<br />
#Wang, J.S., J.A. Logan, M.B. McElroy, B.N. Duncan, I.A. Megretskaia, and R.M. Yantosca, ''A 3-D model analysis of the slowdown and interannual variability in the methane growth rate from 1988 to 1997'', <u>Global Biogeochem. Cycles</u>, '''18''', GB3011, doi:10.1029/2003GB002180, 2004.<br />
<br />
--[[User:Bmy|Bob Y.]] 15:45, 9 April 2014 (EDT)<br />
<br />
== Previous issues that are now resolved ==<br />
<br />
The following bugs and/or issues with the code have now been resolved:<br />
<br />
=== Now call INIT_GLOBAL_CH4 from input_mod.F ===<br />
<br />
'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''<br />
<br />
Prior to [[GEOS-Chem v10-01]], routine <tt>INIT_GLOBAL_CH4</tt> (in module <tt>GeosCore/global_ch4_mod.F</tt>) was called from the main driver routine <tt>main.F</tt> at the start of the simulation. <br />
<br />
In order to make the code more compatible with our [[Grid-Independent GEOS-Chem]] development, we now call <tt>INIT_TAGGED_CH4</tt> from routine <tt>GIGC_INIT_EXTRA</tt> (in module <tt>GeosCore/input_mod.F</tt>).<br />
<br />
--[[User:Bmy|Bob Y.]] 16:59, 30 May 2014 (EDT)<br />
<br />
=== Minor fixes to CH4 simulation for MERRA meteorology ===<br />
<br />
'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''<br />
<br />
We have made a couple of fixes to the CH4 simulation module (<tt>GeosCore/global_ch4_mod.F</tt>) for compatibility with the [[MERRA]] met fields. At lines 1114, and again at line 1503, there were #if blocks that looked like this:<br />
<br />
#if defined( GEOS_5 ) || defined( GEOS_FP )<br />
<br />
but these should have been:<br />
<br />
#if defined( GEOS_5 ) || defined( GEOS_FP ) || defined( MERRA )<br />
<br />
Furthermore, in data directory <tt>GEOS_4x5/CH4_201305/wetlands</tt>, we have symbolically linked files:<br />
<br />
GWETTOP.geos5.4x5.YYYY.bpch --> GWETTOP.merra.4x5.YYYY.bpch<br />
TSKIN.geos5.4x5.YYYY.bpch --> TSKIN.merra.4x5.YYYY.bpch<br />
<br />
where <tt>YYYY = { 2004, 2005, 2006, 2007, 2008, 2009, 2010 }</tt>.<br />
<br />
These issues were discovered with the [[GEOS-Chem Unit Tester]].<br />
<br />
--[[User:Bmy|Bob Y.]] 16:59, 30 May 2014 (EDT)<br />
<br />
=== Fixes for wetland emissions ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''These issues were resolved during the [[GEOS-Chem_v9-02#Period_of_public_comment|public comment period]] following the provisional release of GEOS-Chem v9-02 and were included in the official release of [[GEOS-Chem v9-02]] (03 Mar 2014).'''''<br />
<br />
'''''Kevin Wecht''''' wrote:<br />
<br />
:I have some updates/bug fixes to wetland emissions in the methane simulation. Both changes impact global_ch4_mod.F, subroutine WETLAND_EMIS.<br />
<br />
::1. Christopher Pickett-Heaps added a feature that zeroes wetland emissions if snow covers the ground. This was never incorporated into the standard code. It is included in the attached file.<br />
<br />
::2. Parameters in the subroutine are not correct. The following values are the correct and are included in the attached file:<br />
MOIST_SCALE = 0.205<br />
EMIT_FACT = 0.018<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 16:11, 23 January 2014 (EST)<br><br />
--[[User:Bmy|Bob Y.]] 10:25, 4 April 2014 (EDT)<br />
<br />
=== Error reading GWETTOP fields ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
There is a file read error in the current CH4 simulation. We will fix this issue in [[GEOS-Chem v9-01-03]].<br />
<br />
In RICE_EMIS (global_ch4_mod.F), XTAU is reset to the wrong value when GEWTTOP is read. Kevin Wecht provided a fix that accounts for different availabilities of GEOS-4 and GEOS-5 met fields. Prior to setting FILENAME for GWETTOP , add the following:<br />
<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2009 ) YEAR = 2009<br />
#elif defined( GEOS_4 )<br />
IF ( YEAR .LT. 2000 ) YEAR = 2000<br />
IF ( YEAR .GT. 2006 ) YEAR = 2006<br />
#endif<br />
WRITE( CYEAR, '(i4)' ) YEAR<br />
<br />
:Also change:<br />
<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, GET_YEAR() )<br />
<br />
:to:<br />
<br />
XTAU = GET_TAU0( 1, 1, YEAR )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, YEAR )<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 18:06, 2 February 2012 (EST)<br />
<br />
== Unresolved issues ==<br />
<br />
None reported so far.<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 30 March 2012 (EDT)</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=CH4_simulation&diff=19231CH4 simulation2015-02-24T17:07:53Z<p>Alex Turner: /* Authors and collaborators */</p>
<hr />
<div>This page contains information about the methane (CH4) simulation in GEOS-Chem.<br />
<br />
== Overview ==<br />
<br />
=== Authors and collaborators ===<br />
* [mailto:maasakkers@fas.harvard.edu Bram Maasakkers] ''(Harvard)''<br />
* Alex Turner ''(Harvard; aturner [at] fas [dot] harvard [dot] edu)''<br />
* Kevin Wecht ''(formerly @ Harvard)''<br />
* Christopher Pickett-Heaps ''(formerly @ Harvard)''<br />
* Jerome Drevet ''(formerly @ EPFL)''<br />
* James Wang ''(formerly @ Harvard)''<br />
<br />
=== CH4 simulation user groups ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group<br />
!Personnel<br />
!Projects<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/ Harvard University]<br />
|[mailto:maasakkers@fas.harvard.edu Bram Maasakkers]<br>[mailto:aturner@fas.harvard.edu Alex Turner]<br>Kevin Wecht<br />
|North American methane sources<br> <br />
|-valign="top"<br />
<br />
|}<br />
<br />
=== Notes about the methane simulation ===<br />
<br />
:1. '''annual_met.pro:''' The methane simulation uses monthly and annual average skin temperature and soil moisture values from the met fields. These are calculated offline using IDL ("annual_met.pro"). This file can be found on the ftp site in the methane data directory with the LPJ wetland emission scheme (e.g., "GEOS_0.5x0.666_NA/CH4_201305/wetlands"). The script should work as is for 2004-2011, however we don't currently have the met data for 2012 so you may need to modify "global_ch4_mod.F" if you're interested in 2012 or 2013.<br />
::: '''Subroutine "WETLAND_EMIS"<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
::: '''Subroutine "RICE_EMIS"<br />
! Get annual and monthly mean soil wetness from GEOS<br />
! One file contains both monthly and annual mean GWETTOP<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
:2. '''Seasonality of Rice Emissions:''' Seasonality in the rice emissions is imposed through annual and monthly average soil moisture values. This works reasonably well for major rice growing areas like South/East Asia where rice paddies are rain-fed, but it fails in other regions. For example, California rice paddies are irrigated and crops are grown in the summer, precisely when the natural soil is the driest. You can enter the "global_ch4_mod.F", subroutine "RICE_EMIS", and impose any seasonality you want on the annual emission rates from EDGAR.<br />
<br />
:3. '''Potential Global Mean Bias:''' The methane simulation may not simulate global average concentrations accurately. That is, you may have a mean bias of up to +/-30ppbv when you compare the simulation to observations. A global mean bias means that the model has a slight imbalance between the sources and sinks relative to the world. You may want to consider removing this mean bias before analyzing your model concentrations.<br />
<br />
--[[User:Alex Turner|Alex Turner]] 11:01, 24 January 2014 (EST)<br />
<br />
== Recent science updates ==<br />
<br />
The following updates were recently added into the GEOS-Chem CH4 simulation:<br />
<br />
=== Update CH4 emissions to EDGAR v4.2 ===<br />
<br />
The CH4 simulation now uses emissions from the EDGAR v4.2 inventory.<br />
<br />
==== In GEOS-Chem v10-01 and newer versions ====<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, EDGAR v4.2 CH4 emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CH4/v2014-09/README new emission data files for the CH4 simulation] (in [http://ferret.wrc.noaa.gov/noaa_coop/coop_cdf_profile.html COARDS-compliant netCDF format]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 12:17, 17 February 2015 (EST)<br />
<br />
==== In GEOS-Chem versions prior to v10-01 ====<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02m|v9-02m]] and approved on 30 Jul 2013.'''''<br />
'''''This update is included in Adjoint [[GEOS-Chem_Adjoint_v35 | v35d]].'''''<br />
<br />
Kevin Wecht has prepared EDGAR v4.2 emissions of methane for 2004-2008. The data files are available at:<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/CH4_201305/<br />
<br />
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.<br />
<br />
Modifications to subroutines <tt>RICE_EMIS</tt> and <tt>ASEASONAL_ANTHRO_EMIS</tt> in <tt>global_ch4_mod.F</tt> include changing the directory names and updating CYEAR and XTAU as follows:<br />
<br />
WRITE( CYEAR, '(i4)' ) GET_YEAR()<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
<br />
IF ( GET_YEAR() .LT. 2004 ) THEN<br />
CYEAR='2004'<br />
XTAU = GET_TAU0( 1, 1, 2004 )<br />
ENDIF<br />
IF ( GET_YEAR() .GT. 2008 ) THEN<br />
CYEAR='2008'<br />
XTAU = GET_TAU0( 1, 1, 2008 )<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:53, 2 July 2013 (EDT)<br />
<br />
=== Update methane emissions and add capability for North America nested grid ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
'''''Kevin Wecht wrote:'''''<br />
<br />
:I have some GEOS-Chem methane updates that I'd like to add to the standard code. <br />
<br />
:#GFED emissions - I've updated GFED-2 and GFED-3 biomass burning to include methane emissions.<br />
:#Methane simulation - I've updated emissions and error catches to make the simulation compatible with the nested simulation over North America. I added linearized CH4 chemistry from GMI output (CH4 loss frequencies generated by Lee Murray). These changes should be made to the data directory:<br />
<br />
:::a. Replace Carbon_soil, Carbon_litter, and Wetfrac files in data directory (for all horizontal resolutions)<br />
:::b. Add 2010-2011 TSKIN and GWETTOP files to data directory (for all horizontal resolutions)<br />
:::c. Add nested north american OH files to OH directory<br />
:::d. Add biofuel emissions to data directory (for all horizontal resolutions)<br />
:::e. Add all emission files to data directory for nested North America simulation<br />
<br />
The [[CH4_simulation#Error_reading_GWETTOP_fields|error in reading GWETTOP fields]] is also fixed in this update.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:35, 2 February 2012 (EST)<br />
<br />
== Validation ==<br />
<br />
TBD<br />
<br />
== References ==<br />
<br />
#Wecht, K.J., D.J. Jacob, C. Frankenberg, Z. Jiang, and D.R. Blake, ''Mapping of North America methane emissions with high spatial resolution by inversion of SCIAMACHY satellite data'', submitted to <u>J. Geophys. Res.</u>, 2014.<br />
#Wecht, K.J., D.J. Jacob, M.P. Sulprizio, G.W. Santoni, S.C. Wofsy, R. Parker, H. Bösch, and J.R. Worden, ''Spatially resolving methane emissions in California: constraints from the CalNex aircraft campaign and from present (GOSAT, TES) and future (TROPOMI, geostationary) satellite observations'', <u>Atm. Chem. Phys. Discuss.</u>, '''14''', 4119-4198, doi:10.5194/acpd-14-4119-2014, 2014.<br />
#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'', <u>Atmos. Chem. Phys.</u>, '''12''', 1823-1832, 2012.<br />
#Pickett-Heaps, C.A., D.J. Jacob, K.J. Wecht, E.A. Kort, S.C. Wofsy, G.S. Diskin, D.E.J. Worthy, J.O. Kaplan, I. Bey, and J. Drevet, ''Magnitude of seasonality of wetland methane emissions from the Hudson Bay Lowlands (Canada)'', <u>Atmos. Chem. Phys.</u>, '''11(8)''', 3773-3779, doi:10.5194/acp-11-3773-2011, 2011.<br />
#Wang, J.S., J.A. Logan, M.B. McElroy, B.N. Duncan, I.A. Megretskaia, and R.M. Yantosca, ''A 3-D model analysis of the slowdown and interannual variability in the methane growth rate from 1988 to 1997'', <u>Global Biogeochem. Cycles</u>, '''18''', GB3011, doi:10.1029/2003GB002180, 2004.<br />
<br />
--[[User:Bmy|Bob Y.]] 15:45, 9 April 2014 (EDT)<br />
<br />
== Previous issues that are now resolved ==<br />
<br />
The following bugs and/or issues with the code have now been resolved:<br />
<br />
=== Now call INIT_GLOBAL_CH4 from input_mod.F ===<br />
<br />
'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''<br />
<br />
Prior to [[GEOS-Chem v10-01]], routine <tt>INIT_GLOBAL_CH4</tt> (in module <tt>GeosCore/global_ch4_mod.F</tt>) was called from the main driver routine <tt>main.F</tt> at the start of the simulation. <br />
<br />
In order to make the code more compatible with our [[Grid-Independent GEOS-Chem]] development, we now call <tt>INIT_TAGGED_CH4</tt> from routine <tt>GIGC_INIT_EXTRA</tt> (in module <tt>GeosCore/input_mod.F</tt>).<br />
<br />
--[[User:Bmy|Bob Y.]] 16:59, 30 May 2014 (EDT)<br />
<br />
=== Minor fixes to CH4 simulation for MERRA meteorology ===<br />
<br />
'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''<br />
<br />
We have made a couple of fixes to the CH4 simulation module (<tt>GeosCore/global_ch4_mod.F</tt>) for compatibility with the [[MERRA]] met fields. At lines 1114, and again at line 1503, there were #if blocks that looked like this:<br />
<br />
#if defined( GEOS_5 ) || defined( GEOS_FP )<br />
<br />
but these should have been:<br />
<br />
#if defined( GEOS_5 ) || defined( GEOS_FP ) || defined( MERRA )<br />
<br />
Furthermore, in data directory <tt>GEOS_4x5/CH4_201305/wetlands</tt>, we have symbolically linked files:<br />
<br />
GWETTOP.geos5.4x5.YYYY.bpch --> GWETTOP.merra.4x5.YYYY.bpch<br />
TSKIN.geos5.4x5.YYYY.bpch --> TSKIN.merra.4x5.YYYY.bpch<br />
<br />
where <tt>YYYY = { 2004, 2005, 2006, 2007, 2008, 2009, 2010 }</tt>.<br />
<br />
These issues were discovered with the [[GEOS-Chem Unit Tester]].<br />
<br />
--[[User:Bmy|Bob Y.]] 16:59, 30 May 2014 (EDT)<br />
<br />
=== Fixes for wetland emissions ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''These issues were resolved during the [[GEOS-Chem_v9-02#Period_of_public_comment|public comment period]] following the provisional release of GEOS-Chem v9-02 and were included in the official release of [[GEOS-Chem v9-02]] (03 Mar 2014).'''''<br />
<br />
'''''Kevin Wecht''''' wrote:<br />
<br />
:I have some updates/bug fixes to wetland emissions in the methane simulation. Both changes impact global_ch4_mod.F, subroutine WETLAND_EMIS.<br />
<br />
::1. Christopher Pickett-Heaps added a feature that zeroes wetland emissions if snow covers the ground. This was never incorporated into the standard code. It is included in the attached file.<br />
<br />
::2. Parameters in the subroutine are not correct. The following values are the correct and are included in the attached file:<br />
MOIST_SCALE = 0.205<br />
EMIT_FACT = 0.018<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 16:11, 23 January 2014 (EST)<br><br />
--[[User:Bmy|Bob Y.]] 10:25, 4 April 2014 (EDT)<br />
<br />
=== Error reading GWETTOP fields ===<br />
<br />
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>In [[GEOS-Chem v10-01]] and newer versions, CH4 emissions are implemented via the [[HEMCO|HEMCO emissions component]].</p><p>&mdash; Bob Yantosca, 17 February 2015</p>'''</div><br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
There is a file read error in the current CH4 simulation. We will fix this issue in [[GEOS-Chem v9-01-03]].<br />
<br />
In RICE_EMIS (global_ch4_mod.F), XTAU is reset to the wrong value when GEWTTOP is read. Kevin Wecht provided a fix that accounts for different availabilities of GEOS-4 and GEOS-5 met fields. Prior to setting FILENAME for GWETTOP , add the following:<br />
<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2009 ) YEAR = 2009<br />
#elif defined( GEOS_4 )<br />
IF ( YEAR .LT. 2000 ) YEAR = 2000<br />
IF ( YEAR .GT. 2006 ) YEAR = 2006<br />
#endif<br />
WRITE( CYEAR, '(i4)' ) YEAR<br />
<br />
:Also change:<br />
<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, GET_YEAR() )<br />
<br />
:to:<br />
<br />
XTAU = GET_TAU0( 1, 1, YEAR )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, YEAR )<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 18:06, 2 February 2012 (EST)<br />
<br />
== Unresolved issues ==<br />
<br />
None reported so far.<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 30 March 2012 (EDT)</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_Adjoint&diff=18499GEOS-Chem Adjoint2015-01-13T14:41:05Z<p>Alex Turner: /* Journal Articles */</p>
<hr />
<div><big><big><strong>Adjoint Working Group</strong></big></big><br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
<br />
|-<br />
|bgcolor="#CCCCCC"|'''Adjoint Model Scientist'''<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|bgcolor="#CCCCCC"|'''GC adjoint support team'''<br />
|[mailto:yanko.davila@colorado.edu Yanko Davila], [mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez]<br />
|-<br />
|bgcolor="#CCCCCC"|'''Adjoint Working Group email list'''<br />
|<tt>geos-chem-adjoint@seas.harvard.edu</tt><br />
|-<br />
|bgcolor="#CCCCCC"|'''To subscribe to email list'''<br />
|Send email to [mailto:geos-chem-adjoint-join@seas.harvard.edu <tt>geos-chem-adjoint-join@seas.harvard.edu</tt>]<br />
|-<br />
|bgcolor="#CCCCCC"|'''To unsubscribe from email list'''<br />
|Send email to [mailto:geos-chem-adjoint-leave@seas.harvard.edu <tt>geos-chem-adjoint-leave@seas.harvard.edu</tt>]<br />
|}<br />
<br />
== Historical Development ==<br />
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. <br />
<br />
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.<br />
<br />
== Forward Model Code ==<br />
<br />
The forward model on which the adjoint is based originally corresponded to GEOS-Chem v8-02-01. It was subsequently updated as follows:<br />
<br />
* KPP solver for gas-phase chemistry (as in GCv8-02-03)<br />
* Implement Bond 2007 BC/OC emissions (as in GCv8-02-02)<br />
* Apply bug fixes from GCv8-02-02 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-02#Previous_issues_now_resolved_in_v8-02-02 here]<br />
* Apply bug fixes from GCv8-02-03 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-03#Previous_issues_now_resolved_in_v8-02-03 here]<br />
* Apply bug fixes from GCv8-02-04 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-04#Previous_issues_now_resolved_in_v8-02-04 here]<br />
<br />
All bug fixes and model updates were previous listed at the top of inverse_driver.f. We have now switched to documenting the code development cycle here in the wiki, see the following section. <br />
<br />
== Code Versions, Bug Fixes and Developments == <br />
<br />
=== Current GEOS-Chem adjoint version released ===<br />
*[[GEOS-Chem_Adjoint_v35]] (You will download this version when you check out.)<br />
<br />
=== Previous GEOS-Chem adjoint versions released ===<br />
*[[GEOS-Chem_Adjoint_v34]]<br />
*[[GEOS-Chem_Adjoint_v33]] <br />
*[[GEOS-Chem_Adjoint_v32]]<br />
*[[GEOS-Chem_Adjoint_v31]]<br />
<br />
== Summary of Main Adjoint Code Supported Features ==<br />
<br />
=== Features === <br />
* Meteorological fields<br />
** GEOS-3 <i>needs testing</i><br />
** GEOS-4<br />
** GEOS-5 <br />
* model resolution<br />
** 4 x 5<br />
** 2 x 2.5 <br />
** Nested Asia and NA<br />
* Forward model processes<br />
** convection<br />
** advection<br />
** PBL mixing<br />
** dry deposition<br />
** wet deposition<br />
** strat / trop exchange with LINOZ and new GMI strat chem (v9-01-03)<br />
** NOy up fluxes (now replaced with new GMI strat chem)<br />
** aerosols <br />
*** inorganic aerosol thermodynamics with RPMARES<br />
*** inorganic aerosol thermodynamics with ISORROPIA <i> in progress </i><br />
*** sulfate chemistry <br />
*** BC<br />
*** SOA, Dust, sea salt <i> needs doing </i><br />
*** aerosol surface area feedbacks <i> needs updating </i><br />
*** aerosol optical feedbacks <i> needs doing </i><br />
** emissions<br />
*** all standard emissions included<br />
* Simulation modes<br />
** full chemistry<br />
** tagged CO<br />
** tagged Ox <br />
** CH4<br />
** offline aerosols (for BC and dust only)<br />
** CO2<br />
* Observational Operators<br />
** MOPITT CO column<br />
** SCIAMACHY CO column<br />
** AIRS CO column<br />
** IMPROVE BC<br />
** CASTNet (NH4+) <i> needs updating </i> <br />
** GOME / SCIAMACHY NO2 column <i> needs updating </i> <br />
*** using KNMI retrieval (Henze)<br />
*** using Dalhousie retrieval (Shim)<br />
** SCIAMACHY/OMI NO2<br />
*** using Dalhousie retrieval (Bousserez, Padmanabhan)<br />
** TES NH3 <br />
** TES O3 <br />
** GOSAT CO2 <br />
** MLS O3 and TES CO2 <i> in progress </i><br />
* Control parameters<br />
** Initial Conditions scaling factors (linear or log)<br />
** Emissions scaling factors (linear or log) <br />
*** NH3, primary BC/OC, SO2: anthropogenic, natural, bioburn, biomass, ship<br />
*** NOx: soil, aircraft, anthropogenic, biofuel, bioburn<br />
*** Lightning NOx: injection height, yield <i> in progress </i><br />
*** all other gas-phase tracers: anthropogenic, biofuel, bioburn <br />
* Adjoint sensitivities<br />
** w.r.t. all implemented control parameters<br />
** w.r.t Reaction Rate Parameters <br />
** w.r.t all emissions <br />
** of AQ attainment metrics <i> needs updating </i><br />
** of spatiotemporally averaged species concentrations (e.g., arctic O3) <br />
* Other<br />
** Inverse Hessian approximation <br />
** off-diagonal covariance matrices <i> needs updating </i><br />
** 3D-Var <i> needs updating </i><br />
<br />
Features may be qualified as: <br />
* <i>needs testing</i>: an implemented feature that we haven't fully used yet<br />
* <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<br />
* <i>needs doing</i>: a feature nobody has tackled the adjoint of yet<br />
* <i>in progress</i>: a feature currently under development <br />
* <i>in pipeline</i>: a feature which has been submitted and awaiting integration into the CVS repository<br />
<br />
=== Primary code developers ===<br />
Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze<br />
<br />
=== Adjoint model lead scientist ===<br />
Daven Henze<br />
<br />
<br />
<br />
== Resources ==<br />
<br />
=== User's guide ===<br />
A user's guide v35 is available. [http://adjoint.colorado.edu/~yanko/gcadj_std/GC_adj_man.pdf User's Guide v35] <br />
<br />
Previous version v32-v33 available at [http://adjoint.colorado.edu/~daven/gcadj_std/GC_adj_man.pdf User's Guide v32]<br />
<br />
Quick Introduction to GitLab is available at [http://adjoint.colorado.edu/~yanko/gcadj_std/GitLab_Tutorial.pdf GitLab Tutorial]<br />
<br />
=== Code flowchart ===<br />
Meemong Lee has created a detailed flowchart of the inverse model code structure. http://adjoint.colorado.edu/~daven/gcadj_std/flowchart.pdf<br />
<br />
=== Plotting tools ===<br />
<br />
Some IDL and MATLAB routines for plotting benchmark results. http://adjoint.colorado.edu/~daven/gcadj_std/tools.tar.gz<br />
<br />
=== Background papers and presentations ===<br />
<br />
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<br />
<br />
== Distribution and Use ==<br />
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.]] <br />
<br />
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. <br />
<br />
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.<br />
<br />
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 tuned 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 comunity just send Daven Henze your [[Using_Git_with_GEOS-Chem#Sharing_your_revisions_with_others_.28and_vice_versa.29|patch]] and we'll take care of the rest.<br />
<br />
=== Quick guide to GIT === <br />
As of version 34 we started using git versioning system and the GitLab web interface. We prepared [http://adjoint.colorado.edu/~yanko/gcadj_std/GitLab_Tutorial.pdf 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., [http://git-scm.com/documentation GIT Documentation] or [http://www.kernel.org/pub/software/scm/git/docs/git.html GIT Manual Page]). <br />
<br />
<br />
Useful GIT commands: <br />
<br />
Initial download:<br />
git clone ssh://git@adjoint.colorado.edu:2222/yanko.davila/gcadj_std.git<br />
<br />
Status of project vs the current repository:<br />
git status<br />
<br />
Check difference of files (differences have colors for easy reading)<br />
git diff --word-diff=color <wildcard> [<wildcard>] <path>/foo_mod.f<br />
<br />
Checkout specific version<br />
git checkout <wildcard><br />
<br />
Replacing a file with the newest version from the repository:<br />
git checkout origin/master -- <path>/foo_mod.f<br />
<br />
Merging changes in a file: ([http://www.kernel.org/pub/software/scm/git/docs/git-merge.html Reference])<br />
git merge -m <wildcard> <br />
<br />
Comitting<br />
git commit -a<br />
<br />
Tagging a version<br />
git tag -a TAGNAME<br />
<br />
Deleting a tag<br />
git tag -d TAGNAME<br />
git push origin :refs/tags/TAGNAME<br />
<br />
Saving changes to repository<br />
git push<br />
<br />
Saving tags to repository<br />
git push --tags<br />
<br />
List the history of a file:<br />
git log -- <path>/foo_mod.f<br />
<br />
Add a file to the repository<br />
git add <file_name><br />
<br />
Delete a file from the repository<br />
git rm <file_name><br />
<br />
Determine current version<br />
git show HEAD [ | grep commit]<br />
<br />
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.<br />
git pull --rebase<br />
<br />
There are several wildcards that you can use on git for example:<br/><br />
''"origin/master"'' - Latest version on the repository <br/><br />
''"HEAD"'' - Latest version as of your last download <br/><br />
''"[http://adjoint.colorado.edu:8080/gcadj_std/commits/72773d7b1a7bd757957d2c186acb3dbb107d5323 v33i]"'' - Specific TAG, find all tag names on GitLab<br/><br />
''"[http://adjoint.colorado.edu:8080/gcadj_std/commits/32d5c926ef529c1dfc640c9dec4a925b24db575c 32d5c926e]"'' - Specific COMMIT, find all commit numbers on GitLab <br/><br />
<br />
[[Using_Git_with_GEOS-Chem|Here is the foward model documentation of git.]]<br />
<br />
=== Backward compatibility (CVS) === <br />
<br />
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]]<br />
<br />
== Crediting GEOS-Chem adjoint developers ==<br />
<br />
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. <br />
<br />
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:<br />
* (v35) HTAP Emissions Inventory. Kateryna Lapina, Daven Henze and Yanko Davila, CU Boulder.<br />
* (v35) NEI2008 Emissions Inventory. Katie Travis; Fabien Paulot, Harvard; Hyungmin Lee, and Daven Henze, CU Boulder. <br />
* (v35) Deposition based cost function. Fabien Paulot, Harvard; Daven Henze and Yanko Davila, CU Boulder. <br />
* (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. <br />
* (v34) ISOROPIA II adjoint. Developer: Shannon Capps, EPA.<br />
* (v34) Off-diagonal covariance error matrices implementation. Developers: Nicolas Bousserez, CU Boulder; Kumaresh; Yanko Davila, CU Boulder. <br />
* (v32) Nested full chemistry adjoint. Developers: Zhe Jiang, University of Toronto; Daven Henze, CU Boulder.<br />
<br />
<br />
Citation of the appropriate [[GEOS-Chem_Adjoint#Journal_Articles|journal articles]] for mature developments is also encouraged, as well as considering aspects of [http://acmg.seas.harvard.edu/geos/geos_credit.html co-authorship for the forward model]. <br />
<br />
Overall, if you have any questions about authorship, even for a conference presentation, please contact Daven Henze.<br />
<br />
== Current GEOS-Chem Adjoint Research Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group <br />
!Description <br />
!Contact Person<br />
|-<br />
|CU Boulder<br />
|Aerosol precursors, CO2, O3; general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|CU Boulder<br />
|Inverse modeling/optimization; CO2 fluxes inversion (CMS project); general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Nicolas Bousserez]<br />
|-<br />
|CU Boulder<br />
|Identifying long-range sources of atmospheric pollutants utilizing an adjoint method<br />
|[mailto:alicia.camacho@valpo.edu Alicia Camacho]<br />
|-<br />
|CU Boulder<br />
|Sensitivity of nitrate deposition over Antarctica including stratospheric tracers<br />
|[mailto:hyungmin.lee@colorado.edu Hyung-Min Lee]<br />
|-<br />
|CU Boulder<br />
|GEOS-Chem Research<br />
|[mailto:carl.husmann@colorado.edu Carl Husmann]<br />
|-<br />
|CU Boulder<br />
|Constraints on Aerosol Sources<br />
|[mailto:zhen.qu@colorado.edu Zhen Qu]<br />
|-<br />
|Harvard<br />
|Methane<br />
|Alex Turner, aturner [at] fas.harvard.edu<br />
|-<br />
|Harvard<br />
|Methane<br />
|Bram Maasakkers, maasakkers [at] seas.harvard.edu<br />
|-<br />
|Harvard<br />
|Smoke Emissions in SE Asia<br />
|Patrick Kim, kim68 [at] fas.harvard.edu<br />
|-<br />
|Harvard<br />
|Harvard Emissions Component (HEMCO)<br />
|[mailto:ckeller@seas.harvard.edu Christoph Keller]<br />
|-<br />
|Purdue University<br />
|Methane (SICAMACHY, AIRS and IASI)<br />
|[mailto:tang16@purdue.edu Jinyun Tang]<br />
|-<br />
|MIT<br />
|Aircraft emissions<br />
|[mailto:jaminkoo@mit.edu Jamin Koo]<br />
|-<br />
|MIT<br />
|Air quality, aircraft emissions and sensitivities<br />
|[mailto:bvconsta@mit.edu Bogdan V. Constantin]<br />
|-<br />
|Princeton<br />
|BC sensitivities, general adjoint code development<br />
|Monika Kopacz, mkopacz [at] princeton.edu<br />
|-<br />
|Dalhousie University<br />
|Lightning NOx emissions and impact on tropical ozone using the adjoint<br />
|[mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez (now at CU-Boulder)]<br />
|-<br />
|Dalhousie University<br />
|Surface NOx emissions inversion using SCIAMACHY/OMI NO2 measurements<br />
|Akhila Padmanabhan akhila [at] dal.ca; Nicolas Bousserez [mailto:Nicolas.Bousserez@colorado.edu] (now at CU-Boulder)<br />
|-<br />
|JPL<br />
|Microwave Limb Sounder (MLS) Ozone assimilation<br />
|[mailto:meemong.lee@jpl.nasa.gov Meemong Lee]<br />
|-<br />
|JPL <br />
| TES ozone assimilation/attribution of ozone radiative forcing<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman]<br />
|-<br />
|University of Edinburgh<br />
|Quantifying the impact of boreal forest fires on tropospheric oxidants over the Atlantic<br />
|[mailto:mark.parrington@ed.ac.uk Mark Parrington]<br />
|-<br />
|US EPA<br />
|Integration with economic models for future emission inventory scenario development<br />
|[mailto:akhtar.farhan@epa.gov Farhan Akhtar]<br />
|-<br />
|Peking University<br />
|Satellite constraints on VOC emissions <br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|-<br />
|Peking University<br />
|Inverse modeling of Hg sources over east Asia<br />
|[mailto:whuanhuanw@gmail.com Huanhuan Wang]<br />
|-<br />
|IAP.CAS<br />
|CO2 assimilation<br />
|[mailto:czh@mail.iap.ac.cn Chen]<br />
|-<br />
|Purdue University<br />
|Feedback between terrestrial ecosystem processes and atmospheric co2 signals<br />
|[mailto:zhuq@purdue.edu Qing Zhu]<br />
|-<br />
|Purdue University<br />
|Feedback between aquatic ecosystem processes and atmospheric CH4 signals<br />
|[mailto:tan80@purdue.edu Zeli Tan]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and reactive nitrogen to precursor emissions<br />
|[mailto:twalker@atmosp.physics.utoronto.ca Thomas Walker]<br />
|-<br />
|University of Toronto<br />
|Adjoint analysis for carbon monoxide <br />
|[mailto:zjiang@atmosp.physics.utoronto.ca Zhe Jiang]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and CO to precursor emissions<br />
|[mailto:cwhaley@atmosp.physics.utoronto.ca Cynthia Whaley]<br />
|-<br />
|Georgia Tech / CU Boulder<br />
|ISORROPIA adjoint development; NH3 assimilation; cloud droplet sensitivities<br />
|[mailto:shannon.capps@colorado.edu Shannon Capps]<br />
|-<br />
|Peking University<br />
|Source attributions of tropospheric ozone over North China<br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|-<br />
|University of Wollongong<br />
|Sensitivity of ozone and adjoint analysis of CO over Australasia.<br />
|[mailto:rb864@uowmail.edu.au Rebecca Buchholz]<br />
|-<br />
|University of Toronto<br />
|CO2 assimilation & transport model bias estimation<br />
|[mailto:mkeller@atmosp.physics.utoronto.ca Martin Keller]<br />
|-<br />
|University of Wisconsin<br />
|CO2 assimilation and forecast & Temperature profile retrieval <br />
|[mailto:wenguang.bai@ssec.wisc.edu Wenguang Bai]<br />
|-<br />
|Dalhousie University<br />
|Sensitivity of global PM2.5-induced mortality to emissions<br />
|[mailto:colin.lee@dal.ca Colin Lee]<br />
|-<br />
|University of Leicester (UK)<br />
|Top-down estimates of Amazon isoprene emissions<br />
|[mailto:mpb14@le.ac.uk Michael Barkley]<br />
|-<br />
|Anyang University<br />
|Aerosol emission modeling in East Asia <br />
|[mailto:koo@anyang.ac.kr Youn Seo Koo]<br />
|-<br />
|Nanjing University<br />
|Inverse modeling of terrestrial ecosystem carbon flux<br />
|[mailto:hengmao.wang@gmail.com Hengmao Wang]<br />
|-<br />
|Tsinghua University<br />
|Nested-gird simulations with the adjoint model<br />
|[mailto:nany12@mails.tsinghua.edu.cn Nan Yang]<br />
|-<br />
|University of Minnesota<br />
|Inverse modeling of VOC sources based on TES and IASI measurements<br />
||[mailto:kcw@umn.edu Kelley Wells], [mailto:dbm@umn.edu Dylan Millet]<br />
|-<br />
|University of Minnesota & CU Boulder<br />
|Inverse modeling of N2O sources<br />
|[mailto:dbm@umn.edu Dylan Millet], [mailto:Daven.Henze@Colorado.EDU Daven Henze]<br />
|-<br />
|Tsinghua University<br />
|Inverse modeling of anthropogenic emissions over East Asia<br />
|[mailto:qiangzhang@tsinghua.edu.cn Qiang Zhang]<br />
|-<br />
|UCLA<br />
|Constrain black carbon emission<br />
|[mailto:qiling@atmos.ucla.edu Ling Qi]<br />
|-<br />
|UCLA<br />
|source attribution of ozone in the western U.S.<br />
|[mailto:gaomei@atmos.ucla.edu Mei Gao]<br />
|-<br />
|NUS<br />
|Effects of emissions on ozone<br />
|[mailto:rentianyang@nus.edu.sg Ren Tianyang]<br />
|-<br />
|University of Toronto<br />
|Methane inverse modeling<br />
|[mailto:stanevich@atmosp.physics.utoronto.ca Ilya Stanevich]<br />
|-<br />
|}<br />
<br />
== Publications ==<br />
<br />
=== Journal Articles ===<br />
<br />
* '''In press or sumbitted'''<br />
**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, submitted to Atmos. Chem. Phys.<br />
**Turner, A. J. and D. J. Jacob, Balancing aggregation and smoothing errors in inverse models, submitted to Atmos. Chem. Phys.<br />
**Lee, C.J., R.V. Martin, D. K. Henze, M. Brauer, A. Cohen, A. van Donkelaar, Sensitivity of global particulate-matter-related mortality to local precursor emissions, Environ. Health Persp., submitted.<br />
**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 estimates for variational inverse problems, submitted.<br />
**Liu, J., K. Bowman, M. Lee, D. K. Henze, N. Bousserez, H. Brix, D. Menemenlis, L. Ott, S. Pawson, R. Nassar, D. Jones, and J. Collatz, Carbon Monitoring System Flux estimation and attribution (CMS-Flux): Impact of ACOS-GOSAT XCO2 sampling on the inference of terrestrial biospheric sources and sinks, Tellus B, in press.<br />
<br />
* '''2014'''<br />
** 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<br />
**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.<br />
**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<br />
**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<br />
**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<br />
<br />
* '''2013'''<br />
**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<br />
**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<br />
**Xu, X., J. Wang, D. K. Henze, W. Qu, M. Kopacz, 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.<br />
**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.<br />
**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.<br />
**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.<br />
**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<br />
**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<br />
**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<br />
<br />
* '''2012'''<br />
**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.<br />
**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.<br />
**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.<br />
**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.<br />
**Paulot, F., D. K. Henze, and P. O. Wennberg, Impact of the isoprene photochemical cascade on tropical ozone, Atmos. Chem. Phys., 12, 1307-1325.<br />
**Singh, K. and A. Sandu, 2012: Variational chemical data assimilation with approximate adjoints. Computers and Geosciences, 40, 10-18.<br />
**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.<br />
**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.<br />
**Wang, J., X. Xu, D. K. Henze, Q. Ji, S.-C. Tsay, 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.<br />
**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.<br />
**Singh, K. and A. Sandu (2012). "Variational chemical data assimilation with approximate adjoints." Computers and Geosciences 40: 10-18.<br />
<br />
* '''2011'''<br />
**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.<br />
**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.<br />
**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.<br />
<br />
* '''2010'''<br />
**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.<br />
**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.<br />
**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<br />
**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<br />
<br />
* '''2009'''<br />
**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.<br />
**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.<br />
**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.<br />
**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.<br />
**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.<br />
<br />
* '''2007'''<br />
**Henze, D. K., A. Hakami and J. H. Seinfeld (2007), Development of the adjoint of GEOS-Chem, Atmos. Chem. Phys., 7, 2413-2433.<br />
<br />
=== Conference proceedings === <br />
* 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<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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<br />
<br />
* 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</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_Adjoint&diff=18498GEOS-Chem Adjoint2015-01-13T14:37:42Z<p>Alex Turner: /* Current GEOS-Chem Adjoint Research Projects (please add yours!) */</p>
<hr />
<div><big><big><strong>Adjoint Working Group</strong></big></big><br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
<br />
|-<br />
|bgcolor="#CCCCCC"|'''Adjoint Model Scientist'''<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|bgcolor="#CCCCCC"|'''GC adjoint support team'''<br />
|[mailto:yanko.davila@colorado.edu Yanko Davila], [mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez]<br />
|-<br />
|bgcolor="#CCCCCC"|'''Adjoint Working Group email list'''<br />
|<tt>geos-chem-adjoint@seas.harvard.edu</tt><br />
|-<br />
|bgcolor="#CCCCCC"|'''To subscribe to email list'''<br />
|Send email to [mailto:geos-chem-adjoint-join@seas.harvard.edu <tt>geos-chem-adjoint-join@seas.harvard.edu</tt>]<br />
|-<br />
|bgcolor="#CCCCCC"|'''To unsubscribe from email list'''<br />
|Send email to [mailto:geos-chem-adjoint-leave@seas.harvard.edu <tt>geos-chem-adjoint-leave@seas.harvard.edu</tt>]<br />
|}<br />
<br />
== Historical Development ==<br />
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. <br />
<br />
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.<br />
<br />
== Forward Model Code ==<br />
<br />
The forward model on which the adjoint is based originally corresponded to GEOS-Chem v8-02-01. It was subsequently updated as follows:<br />
<br />
* KPP solver for gas-phase chemistry (as in GCv8-02-03)<br />
* Implement Bond 2007 BC/OC emissions (as in GCv8-02-02)<br />
* Apply bug fixes from GCv8-02-02 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-02#Previous_issues_now_resolved_in_v8-02-02 here]<br />
* Apply bug fixes from GCv8-02-03 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-03#Previous_issues_now_resolved_in_v8-02-03 here]<br />
* Apply bug fixes from GCv8-02-04 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-04#Previous_issues_now_resolved_in_v8-02-04 here]<br />
<br />
All bug fixes and model updates were previous listed at the top of inverse_driver.f. We have now switched to documenting the code development cycle here in the wiki, see the following section. <br />
<br />
== Code Versions, Bug Fixes and Developments == <br />
<br />
=== Current GEOS-Chem adjoint version released ===<br />
*[[GEOS-Chem_Adjoint_v35]] (You will download this version when you check out.)<br />
<br />
=== Previous GEOS-Chem adjoint versions released ===<br />
*[[GEOS-Chem_Adjoint_v34]]<br />
*[[GEOS-Chem_Adjoint_v33]] <br />
*[[GEOS-Chem_Adjoint_v32]]<br />
*[[GEOS-Chem_Adjoint_v31]]<br />
<br />
== Summary of Main Adjoint Code Supported Features ==<br />
<br />
=== Features === <br />
* Meteorological fields<br />
** GEOS-3 <i>needs testing</i><br />
** GEOS-4<br />
** GEOS-5 <br />
* model resolution<br />
** 4 x 5<br />
** 2 x 2.5 <br />
** Nested Asia and NA<br />
* Forward model processes<br />
** convection<br />
** advection<br />
** PBL mixing<br />
** dry deposition<br />
** wet deposition<br />
** strat / trop exchange with LINOZ and new GMI strat chem (v9-01-03)<br />
** NOy up fluxes (now replaced with new GMI strat chem)<br />
** aerosols <br />
*** inorganic aerosol thermodynamics with RPMARES<br />
*** inorganic aerosol thermodynamics with ISORROPIA <i> in progress </i><br />
*** sulfate chemistry <br />
*** BC<br />
*** SOA, Dust, sea salt <i> needs doing </i><br />
*** aerosol surface area feedbacks <i> needs updating </i><br />
*** aerosol optical feedbacks <i> needs doing </i><br />
** emissions<br />
*** all standard emissions included<br />
* Simulation modes<br />
** full chemistry<br />
** tagged CO<br />
** tagged Ox <br />
** CH4<br />
** offline aerosols (for BC and dust only)<br />
** CO2<br />
* Observational Operators<br />
** MOPITT CO column<br />
** SCIAMACHY CO column<br />
** AIRS CO column<br />
** IMPROVE BC<br />
** CASTNet (NH4+) <i> needs updating </i> <br />
** GOME / SCIAMACHY NO2 column <i> needs updating </i> <br />
*** using KNMI retrieval (Henze)<br />
*** using Dalhousie retrieval (Shim)<br />
** SCIAMACHY/OMI NO2<br />
*** using Dalhousie retrieval (Bousserez, Padmanabhan)<br />
** TES NH3 <br />
** TES O3 <br />
** GOSAT CO2 <br />
** MLS O3 and TES CO2 <i> in progress </i><br />
* Control parameters<br />
** Initial Conditions scaling factors (linear or log)<br />
** Emissions scaling factors (linear or log) <br />
*** NH3, primary BC/OC, SO2: anthropogenic, natural, bioburn, biomass, ship<br />
*** NOx: soil, aircraft, anthropogenic, biofuel, bioburn<br />
*** Lightning NOx: injection height, yield <i> in progress </i><br />
*** all other gas-phase tracers: anthropogenic, biofuel, bioburn <br />
* Adjoint sensitivities<br />
** w.r.t. all implemented control parameters<br />
** w.r.t Reaction Rate Parameters <br />
** w.r.t all emissions <br />
** of AQ attainment metrics <i> needs updating </i><br />
** of spatiotemporally averaged species concentrations (e.g., arctic O3) <br />
* Other<br />
** Inverse Hessian approximation <br />
** off-diagonal covariance matrices <i> needs updating </i><br />
** 3D-Var <i> needs updating </i><br />
<br />
Features may be qualified as: <br />
* <i>needs testing</i>: an implemented feature that we haven't fully used yet<br />
* <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<br />
* <i>needs doing</i>: a feature nobody has tackled the adjoint of yet<br />
* <i>in progress</i>: a feature currently under development <br />
* <i>in pipeline</i>: a feature which has been submitted and awaiting integration into the CVS repository<br />
<br />
=== Primary code developers ===<br />
Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze<br />
<br />
=== Adjoint model lead scientist ===<br />
Daven Henze<br />
<br />
<br />
<br />
== Resources ==<br />
<br />
=== User's guide ===<br />
A user's guide v35 is available. [http://adjoint.colorado.edu/~yanko/gcadj_std/GC_adj_man.pdf User's Guide v35] <br />
<br />
Previous version v32-v33 available at [http://adjoint.colorado.edu/~daven/gcadj_std/GC_adj_man.pdf User's Guide v32]<br />
<br />
Quick Introduction to GitLab is available at [http://adjoint.colorado.edu/~yanko/gcadj_std/GitLab_Tutorial.pdf GitLab Tutorial]<br />
<br />
=== Code flowchart ===<br />
Meemong Lee has created a detailed flowchart of the inverse model code structure. http://adjoint.colorado.edu/~daven/gcadj_std/flowchart.pdf<br />
<br />
=== Plotting tools ===<br />
<br />
Some IDL and MATLAB routines for plotting benchmark results. http://adjoint.colorado.edu/~daven/gcadj_std/tools.tar.gz<br />
<br />
=== Background papers and presentations ===<br />
<br />
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<br />
<br />
== Distribution and Use ==<br />
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.]] <br />
<br />
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. <br />
<br />
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.<br />
<br />
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 tuned 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 comunity just send Daven Henze your [[Using_Git_with_GEOS-Chem#Sharing_your_revisions_with_others_.28and_vice_versa.29|patch]] and we'll take care of the rest.<br />
<br />
=== Quick guide to GIT === <br />
As of version 34 we started using git versioning system and the GitLab web interface. We prepared [http://adjoint.colorado.edu/~yanko/gcadj_std/GitLab_Tutorial.pdf 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., [http://git-scm.com/documentation GIT Documentation] or [http://www.kernel.org/pub/software/scm/git/docs/git.html GIT Manual Page]). <br />
<br />
<br />
Useful GIT commands: <br />
<br />
Initial download:<br />
git clone ssh://git@adjoint.colorado.edu:2222/yanko.davila/gcadj_std.git<br />
<br />
Status of project vs the current repository:<br />
git status<br />
<br />
Check difference of files (differences have colors for easy reading)<br />
git diff --word-diff=color <wildcard> [<wildcard>] <path>/foo_mod.f<br />
<br />
Checkout specific version<br />
git checkout <wildcard><br />
<br />
Replacing a file with the newest version from the repository:<br />
git checkout origin/master -- <path>/foo_mod.f<br />
<br />
Merging changes in a file: ([http://www.kernel.org/pub/software/scm/git/docs/git-merge.html Reference])<br />
git merge -m <wildcard> <br />
<br />
Comitting<br />
git commit -a<br />
<br />
Tagging a version<br />
git tag -a TAGNAME<br />
<br />
Deleting a tag<br />
git tag -d TAGNAME<br />
git push origin :refs/tags/TAGNAME<br />
<br />
Saving changes to repository<br />
git push<br />
<br />
Saving tags to repository<br />
git push --tags<br />
<br />
List the history of a file:<br />
git log -- <path>/foo_mod.f<br />
<br />
Add a file to the repository<br />
git add <file_name><br />
<br />
Delete a file from the repository<br />
git rm <file_name><br />
<br />
Determine current version<br />
git show HEAD [ | grep commit]<br />
<br />
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.<br />
git pull --rebase<br />
<br />
There are several wildcards that you can use on git for example:<br/><br />
''"origin/master"'' - Latest version on the repository <br/><br />
''"HEAD"'' - Latest version as of your last download <br/><br />
''"[http://adjoint.colorado.edu:8080/gcadj_std/commits/72773d7b1a7bd757957d2c186acb3dbb107d5323 v33i]"'' - Specific TAG, find all tag names on GitLab<br/><br />
''"[http://adjoint.colorado.edu:8080/gcadj_std/commits/32d5c926ef529c1dfc640c9dec4a925b24db575c 32d5c926e]"'' - Specific COMMIT, find all commit numbers on GitLab <br/><br />
<br />
[[Using_Git_with_GEOS-Chem|Here is the foward model documentation of git.]]<br />
<br />
=== Backward compatibility (CVS) === <br />
<br />
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]]<br />
<br />
== Crediting GEOS-Chem adjoint developers ==<br />
<br />
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. <br />
<br />
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:<br />
* (v35) HTAP Emissions Inventory. Kateryna Lapina, Daven Henze and Yanko Davila, CU Boulder.<br />
* (v35) NEI2008 Emissions Inventory. Katie Travis; Fabien Paulot, Harvard; Hyungmin Lee, and Daven Henze, CU Boulder. <br />
* (v35) Deposition based cost function. Fabien Paulot, Harvard; Daven Henze and Yanko Davila, CU Boulder. <br />
* (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. <br />
* (v34) ISOROPIA II adjoint. Developer: Shannon Capps, EPA.<br />
* (v34) Off-diagonal covariance error matrices implementation. Developers: Nicolas Bousserez, CU Boulder; Kumaresh; Yanko Davila, CU Boulder. <br />
* (v32) Nested full chemistry adjoint. Developers: Zhe Jiang, University of Toronto; Daven Henze, CU Boulder.<br />
<br />
<br />
Citation of the appropriate [[GEOS-Chem_Adjoint#Journal_Articles|journal articles]] for mature developments is also encouraged, as well as considering aspects of [http://acmg.seas.harvard.edu/geos/geos_credit.html co-authorship for the forward model]. <br />
<br />
Overall, if you have any questions about authorship, even for a conference presentation, please contact Daven Henze.<br />
<br />
== Current GEOS-Chem Adjoint Research Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group <br />
!Description <br />
!Contact Person<br />
|-<br />
|CU Boulder<br />
|Aerosol precursors, CO2, O3; general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|CU Boulder<br />
|Inverse modeling/optimization; CO2 fluxes inversion (CMS project); general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Nicolas Bousserez]<br />
|-<br />
|CU Boulder<br />
|Identifying long-range sources of atmospheric pollutants utilizing an adjoint method<br />
|[mailto:alicia.camacho@valpo.edu Alicia Camacho]<br />
|-<br />
|CU Boulder<br />
|Sensitivity of nitrate deposition over Antarctica including stratospheric tracers<br />
|[mailto:hyungmin.lee@colorado.edu Hyung-Min Lee]<br />
|-<br />
|CU Boulder<br />
|GEOS-Chem Research<br />
|[mailto:carl.husmann@colorado.edu Carl Husmann]<br />
|-<br />
|CU Boulder<br />
|Constraints on Aerosol Sources<br />
|[mailto:zhen.qu@colorado.edu Zhen Qu]<br />
|-<br />
|Harvard<br />
|Methane<br />
|Alex Turner, aturner [at] fas.harvard.edu<br />
|-<br />
|Harvard<br />
|Methane<br />
|Bram Maasakkers, maasakkers [at] seas.harvard.edu<br />
|-<br />
|Harvard<br />
|Smoke Emissions in SE Asia<br />
|Patrick Kim, kim68 [at] fas.harvard.edu<br />
|-<br />
|Harvard<br />
|Harvard Emissions Component (HEMCO)<br />
|[mailto:ckeller@seas.harvard.edu Christoph Keller]<br />
|-<br />
|Purdue University<br />
|Methane (SICAMACHY, AIRS and IASI)<br />
|[mailto:tang16@purdue.edu Jinyun Tang]<br />
|-<br />
|MIT<br />
|Aircraft emissions<br />
|[mailto:jaminkoo@mit.edu Jamin Koo]<br />
|-<br />
|MIT<br />
|Air quality, aircraft emissions and sensitivities<br />
|[mailto:bvconsta@mit.edu Bogdan V. Constantin]<br />
|-<br />
|Princeton<br />
|BC sensitivities, general adjoint code development<br />
|Monika Kopacz, mkopacz [at] princeton.edu<br />
|-<br />
|Dalhousie University<br />
|Lightning NOx emissions and impact on tropical ozone using the adjoint<br />
|[mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez (now at CU-Boulder)]<br />
|-<br />
|Dalhousie University<br />
|Surface NOx emissions inversion using SCIAMACHY/OMI NO2 measurements<br />
|Akhila Padmanabhan akhila [at] dal.ca; Nicolas Bousserez [mailto:Nicolas.Bousserez@colorado.edu] (now at CU-Boulder)<br />
|-<br />
|JPL<br />
|Microwave Limb Sounder (MLS) Ozone assimilation<br />
|[mailto:meemong.lee@jpl.nasa.gov Meemong Lee]<br />
|-<br />
|JPL <br />
| TES ozone assimilation/attribution of ozone radiative forcing<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman]<br />
|-<br />
|University of Edinburgh<br />
|Quantifying the impact of boreal forest fires on tropospheric oxidants over the Atlantic<br />
|[mailto:mark.parrington@ed.ac.uk Mark Parrington]<br />
|-<br />
|US EPA<br />
|Integration with economic models for future emission inventory scenario development<br />
|[mailto:akhtar.farhan@epa.gov Farhan Akhtar]<br />
|-<br />
|Peking University<br />
|Satellite constraints on VOC emissions <br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|-<br />
|Peking University<br />
|Inverse modeling of Hg sources over east Asia<br />
|[mailto:whuanhuanw@gmail.com Huanhuan Wang]<br />
|-<br />
|IAP.CAS<br />
|CO2 assimilation<br />
|[mailto:czh@mail.iap.ac.cn Chen]<br />
|-<br />
|Purdue University<br />
|Feedback between terrestrial ecosystem processes and atmospheric co2 signals<br />
|[mailto:zhuq@purdue.edu Qing Zhu]<br />
|-<br />
|Purdue University<br />
|Feedback between aquatic ecosystem processes and atmospheric CH4 signals<br />
|[mailto:tan80@purdue.edu Zeli Tan]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and reactive nitrogen to precursor emissions<br />
|[mailto:twalker@atmosp.physics.utoronto.ca Thomas Walker]<br />
|-<br />
|University of Toronto<br />
|Adjoint analysis for carbon monoxide <br />
|[mailto:zjiang@atmosp.physics.utoronto.ca Zhe Jiang]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and CO to precursor emissions<br />
|[mailto:cwhaley@atmosp.physics.utoronto.ca Cynthia Whaley]<br />
|-<br />
|Georgia Tech / CU Boulder<br />
|ISORROPIA adjoint development; NH3 assimilation; cloud droplet sensitivities<br />
|[mailto:shannon.capps@colorado.edu Shannon Capps]<br />
|-<br />
|Peking University<br />
|Source attributions of tropospheric ozone over North China<br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|-<br />
|University of Wollongong<br />
|Sensitivity of ozone and adjoint analysis of CO over Australasia.<br />
|[mailto:rb864@uowmail.edu.au Rebecca Buchholz]<br />
|-<br />
|University of Toronto<br />
|CO2 assimilation & transport model bias estimation<br />
|[mailto:mkeller@atmosp.physics.utoronto.ca Martin Keller]<br />
|-<br />
|University of Wisconsin<br />
|CO2 assimilation and forecast & Temperature profile retrieval <br />
|[mailto:wenguang.bai@ssec.wisc.edu Wenguang Bai]<br />
|-<br />
|Dalhousie University<br />
|Sensitivity of global PM2.5-induced mortality to emissions<br />
|[mailto:colin.lee@dal.ca Colin Lee]<br />
|-<br />
|University of Leicester (UK)<br />
|Top-down estimates of Amazon isoprene emissions<br />
|[mailto:mpb14@le.ac.uk Michael Barkley]<br />
|-<br />
|Anyang University<br />
|Aerosol emission modeling in East Asia <br />
|[mailto:koo@anyang.ac.kr Youn Seo Koo]<br />
|-<br />
|Nanjing University<br />
|Inverse modeling of terrestrial ecosystem carbon flux<br />
|[mailto:hengmao.wang@gmail.com Hengmao Wang]<br />
|-<br />
|Tsinghua University<br />
|Nested-gird simulations with the adjoint model<br />
|[mailto:nany12@mails.tsinghua.edu.cn Nan Yang]<br />
|-<br />
|University of Minnesota<br />
|Inverse modeling of VOC sources based on TES and IASI measurements<br />
||[mailto:kcw@umn.edu Kelley Wells], [mailto:dbm@umn.edu Dylan Millet]<br />
|-<br />
|University of Minnesota & CU Boulder<br />
|Inverse modeling of N2O sources<br />
|[mailto:dbm@umn.edu Dylan Millet], [mailto:Daven.Henze@Colorado.EDU Daven Henze]<br />
|-<br />
|Tsinghua University<br />
|Inverse modeling of anthropogenic emissions over East Asia<br />
|[mailto:qiangzhang@tsinghua.edu.cn Qiang Zhang]<br />
|-<br />
|UCLA<br />
|Constrain black carbon emission<br />
|[mailto:qiling@atmos.ucla.edu Ling Qi]<br />
|-<br />
|UCLA<br />
|source attribution of ozone in the western U.S.<br />
|[mailto:gaomei@atmos.ucla.edu Mei Gao]<br />
|-<br />
|NUS<br />
|Effects of emissions on ozone<br />
|[mailto:rentianyang@nus.edu.sg Ren Tianyang]<br />
|-<br />
|University of Toronto<br />
|Methane inverse modeling<br />
|[mailto:stanevich@atmosp.physics.utoronto.ca Ilya Stanevich]<br />
|-<br />
|}<br />
<br />
== Publications ==<br />
<br />
=== Journal Articles ===<br />
<br />
* '''In press or sumbitted'''<br />
**Lee, C.J., R.V. Martin, D. K. Henze, M. Brauer, A. Cohen, A. van Donkelaar, Sensitivity of global particulate-matter-related mortality to local precursor emissions, Environ. Health Persp., submitted.<br />
**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 estimates for variational inverse problems, submitted.<br />
**Liu, J., K. Bowman, M. Lee, D. K. Henze, N. Bousserez, H. Brix, D. Menemenlis, L. Ott, S. Pawson, R. Nassar, D. Jones, and J. Collatz, Carbon Monitoring System Flux estimation and attribution (CMS-Flux): Impact of ACOS-GOSAT XCO2 sampling on the inference of terrestrial biospheric sources and sinks, Tellus B, in press.<br />
<br />
* '''2014'''<br />
** 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<br />
**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.<br />
**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<br />
**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<br />
**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<br />
<br />
* '''2013'''<br />
**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<br />
**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<br />
**Xu, X., J. Wang, D. K. Henze, W. Qu, M. Kopacz, 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.<br />
**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.<br />
**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.<br />
**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.<br />
**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<br />
**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<br />
**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<br />
<br />
* '''2012'''<br />
**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.<br />
**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.<br />
**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.<br />
**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.<br />
**Paulot, F., D. K. Henze, and P. O. Wennberg, Impact of the isoprene photochemical cascade on tropical ozone, Atmos. Chem. Phys., 12, 1307-1325.<br />
**Singh, K. and A. Sandu, 2012: Variational chemical data assimilation with approximate adjoints. Computers and Geosciences, 40, 10-18.<br />
**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.<br />
**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.<br />
**Wang, J., X. Xu, D. K. Henze, Q. Ji, S.-C. Tsay, 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.<br />
**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.<br />
**Singh, K. and A. Sandu (2012). "Variational chemical data assimilation with approximate adjoints." Computers and Geosciences 40: 10-18.<br />
<br />
* '''2011'''<br />
**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.<br />
**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.<br />
**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.<br />
<br />
* '''2010'''<br />
**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.<br />
**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.<br />
**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<br />
**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<br />
<br />
* '''2009'''<br />
**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.<br />
**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.<br />
**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.<br />
**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.<br />
**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.<br />
<br />
* '''2007'''<br />
**Henze, D. K., A. Hakami and J. H. Seinfeld (2007), Development of the adjoint of GEOS-Chem, Atmos. Chem. Phys., 7, 2413-2433.<br />
<br />
=== Conference proceedings === <br />
* 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<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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<br />
<br />
* 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</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=CH4_simulation&diff=15632CH4 simulation2014-01-24T16:01:14Z<p>Alex Turner: /* Planned updates */</p>
<hr />
<div>This page contains information about the methane (CH4) simulation in GEOS-Chem.<br />
<br />
== Overview ==<br />
<br />
The CH4 simulation in GEOS-Chem ...<br />
<br />
=== Authors and collaborators ===<br />
* [mailto:maasakkers@fas.harvard.edu Bram Maasakkers] ''(Harvard)''<br />
* [mailto:aturner@fas.harvard.edu Alex Turner] ''(Harvard)''<br />
* [mailto:kevin.wecht@gmail.com Kevin Wecht] ''(Harvard)''<br />
* Christopher Pickett-Heaps ''(formerly @ Harvard)''<br />
* Jerome Drevet ''(formerly @ EPFL)''<br />
* James Wang ''(formerly @ Harvard)''<br />
<br />
=== CH4 simulation user groups ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group<br />
!Personnel<br />
!Projects<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/ Harvard University]<br />
|[mailto:maasakkers@fas.harvard.edu Bram Maasakkers]<br>[mailto:aturner@fas.harvard.edu Alex Turner]<br>[mailto:kevin.wecht@gmail.com Kevin Wecht]<br />
|North American methane sources<br> <br />
|-valign="top"<br />
|U. Wollongong<br />
|[mailto:cm700@uow.edu.au Chris Chan Miller]<br />
|Methane sources in tropical Australia<br />
<br />
|}<br />
<br />
== Validation ==<br />
<br />
== Planned updates ==<br />
<br />
=== Update methane emissions and add capability for North America nested grid ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
'''''[mailto:wecht@fas.harvard.edu Kevin Wecht] wrote:'''''<br />
<br />
:I have some GEOS-Chem methane updates that I'd like to add to the standard code. <br />
<br />
:#GFED emissions - I've updated GFED-2 and GFED-3 biomass burning to include methane emissions.<br />
:#Methane simulation - I've updated emissions and error catches to make the simulation compatible with the nested simulation over North America. I added linearized CH4 chemistry from GMI output (CH4 loss frequencies generated by Lee Murray). These changes should be made to the data directory:<br />
<br />
:::a. Replace Carbon_soil, Carbon_litter, and Wetfrac files in data directory (for all horizontal resolutions)<br />
:::b. Add 2010-2011 TSKIN and GWETTOP files to data directory (for all horizontal resolutions)<br />
:::c. Add nested north american OH files to OH directory<br />
:::d. Add biofuel emissions to data directory (for all horizontal resolutions)<br />
:::e. Add all emission files to data directory for nested North America simulation<br />
<br />
The [[CH4_simulation#Error_reading_GWETTOP_fields|error in reading GWETTOP fields]] is also fixed in this update.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:35, 2 February 2012 (EST)<br />
<br />
=== Update CH4 emissions to EDGAR v4.2 ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02m|v9-02m]] and approved on 30 Jul 2013.'''''<br />
<br />
Kevin Wecht has prepared EDGAR v4.2 emissions of methane for 2004-2008. The data files are available at:<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/CH4_201305/<br />
<br />
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.<br />
<br />
Modifications to subroutines <tt>RICE_EMIS</tt> and <tt>ASEASONAL_ANTHRO_EMIS</tt> in <tt>global_ch4_mod.F</tt> include changing the directory names and updating CYEAR and XTAU as follows:<br />
<br />
WRITE( CYEAR, '(i4)' ) GET_YEAR()<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
<br />
IF ( GET_YEAR() .LT. 2004 ) THEN<br />
CYEAR='2004'<br />
XTAU = GET_TAU0( 1, 1, 2004 )<br />
ENDIF<br />
IF ( GET_YEAR() .GT. 2008 ) THEN<br />
CYEAR='2008'<br />
XTAU = GET_TAU0( 1, 1, 2008 )<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:53, 2 July 2013 (EDT)<br />
<br />
=== Fixes for wetland emissions ===<br />
<br />
'''''These issues were resolved during the [[GEOS-Chem_v9-02#Period_of_public_comment|public comment period]] following the provisional release of GEOS-Chem v9-02 and will be included in the official release of [[GEOS-Chem v9-02]].'''''<br />
<br />
'''''[mailto:kevin.wecht@gmail.com Kevin Wecht]''''' wrote:<br />
<br />
:I have some updates/bug fixes to wetland emissions in the methane simulation. Both changes impact global_ch4_mod.F, subroutine WETLAND_EMIS.<br />
<br />
::1. Christopher Pickett-Heaps added a feature that zeroes wetland emissions if snow covers the ground. This was never incorporated into the standard code. It is included in the attached file.<br />
<br />
::2. Parameters in the subroutine are not correct. The following values are the correct and are included in the attached file:<br />
MOIST_SCALE = 0.205<br />
EMIT_FACT = 0.018<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 16:11, 23 January 2014 (EST)<br />
<br />
=== Notes about the methane simulation ===<br />
<br />
:1. '''annual_met.pro:''' The methane simulation uses monthly and annual average skin temperature and soil moisture values from the met fields. These are calculated offline using IDL ("annual_met.pro"). This file can be found on the ftp site in the methane data directory with the LPJ wetland emission scheme (e.g., "GEOS_0.5x0.666_NA/CH4_201305/wetlands"). The script should work as is for 2004-2011, however we don't currently have the met data for 2012 so you may need to modify "global_ch4_mod.F" if you're interested in 2012 or 2013.<br />
::: '''Subroutine "WETLAND_EMIS"<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
::: '''Subroutine "RICE_EMIS"<br />
! Get annual and monthly mean soil wetness from GEOS<br />
! One file contains both monthly and annual mean GWETTOP<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2011 ) YEAR = 2011<br />
<br />
:2. '''Seasonality of Rice Emissions:''' Seasonality in the rice emissions is imposed through annual and monthly average soil moisture values. This works reasonably well for major rice growing areas like South/East Asia where rice paddies are rain-fed, but it fails in other regions. For example, California rice paddies are irrigated and crops are grown in the summer, precisely when the natural soil is the driest. You can enter the "global_ch4_mod.F", subroutine "RICE_EMIS", and impose any seasonality you want on the annual emission rates from EDGAR.<br />
<br />
:3. '''Potential Global Mean Bias:''' The methane simulation may not simulate global average concentrations accurately. That is, you may have a mean bias of up to +/-30ppbv when you compare the simulation to observations. A global mean bias means that the model has a slight imbalance between the sources and sinks relative to the world. You may want to consider removing this mean bias before analyzing your model concentrations.<br />
<br />
--[[User:Alex Turner|Alex Turner]] 11:01, 24 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
== Previous issues that are now resolved ==<br />
<br />
=== Error reading GWETTOP fields ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
There is a file read error in the current CH4 simulation. We will fix this issue in [[GEOS-Chem v9-01-03]].<br />
<br />
In RICE_EMIS (global_ch4_mod.F), XTAU is reset to the wrong value when GEWTTOP is read. Kevin Wecht provided a fix that accounts for different availabilities of GEOS-4 and GEOS-5 met fields. Prior to setting FILENAME for GWETTOP , add the following:<br />
<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2009 ) YEAR = 2009<br />
#elif defined( GEOS_4 )<br />
IF ( YEAR .LT. 2000 ) YEAR = 2000<br />
IF ( YEAR .GT. 2006 ) YEAR = 2006<br />
#endif<br />
WRITE( CYEAR, '(i4)' ) YEAR<br />
<br />
:Also change:<br />
<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, GET_YEAR() )<br />
<br />
:to:<br />
<br />
XTAU = GET_TAU0( 1, 1, YEAR )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, YEAR )<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 18:06, 2 February 2012 (EST)<br />
<br />
== Outstanding Issues ==<br />
<br />
None reported so far.<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 30 March 2012 (EDT)</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=CH4_simulation&diff=15631CH4 simulation2014-01-24T15:27:34Z<p>Alex Turner: /* CH4 simulation user groups */</p>
<hr />
<div>This page contains information about the methane (CH4) simulation in GEOS-Chem.<br />
<br />
== Overview ==<br />
<br />
The CH4 simulation in GEOS-Chem ...<br />
<br />
=== Authors and collaborators ===<br />
* [mailto:maasakkers@fas.harvard.edu Bram Maasakkers] ''(Harvard)''<br />
* [mailto:aturner@fas.harvard.edu Alex Turner] ''(Harvard)''<br />
* [mailto:kevin.wecht@gmail.com Kevin Wecht] ''(Harvard)''<br />
* Christopher Pickett-Heaps ''(formerly @ Harvard)''<br />
* Jerome Drevet ''(formerly @ EPFL)''<br />
* James Wang ''(formerly @ Harvard)''<br />
<br />
=== CH4 simulation user groups ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group<br />
!Personnel<br />
!Projects<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/ Harvard University]<br />
|[mailto:maasakkers@fas.harvard.edu Bram Maasakkers]<br>[mailto:aturner@fas.harvard.edu Alex Turner]<br>[mailto:kevin.wecht@gmail.com Kevin Wecht]<br />
|North American methane sources<br> <br />
|-valign="top"<br />
|U. Wollongong<br />
|[mailto:cm700@uow.edu.au Chris Chan Miller]<br />
|Methane sources in tropical Australia<br />
<br />
|}<br />
<br />
== Validation ==<br />
<br />
== Planned updates ==<br />
<br />
=== Update methane emissions and add capability for North America nested grid ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
'''''[mailto:wecht@fas.harvard.edu Kevin Wecht] wrote:'''''<br />
<br />
:I have some GEOS-Chem methane updates that I'd like to add to the standard code. <br />
<br />
:#GFED emissions - I've updated GFED-2 and GFED-3 biomass burning to include methane emissions.<br />
:#Methane simulation - I've updated emissions and error catches to make the simulation compatible with the nested simulation over North America. I added linearized CH4 chemistry from GMI output (CH4 loss frequencies generated by Lee Murray). These changes should be made to the data directory:<br />
<br />
:::a. Replace Carbon_soil, Carbon_litter, and Wetfrac files in data directory (for all horizontal resolutions)<br />
:::b. Add 2010-2011 TSKIN and GWETTOP files to data directory (for all horizontal resolutions)<br />
:::c. Add nested north american OH files to OH directory<br />
:::d. Add biofuel emissions to data directory (for all horizontal resolutions)<br />
:::e. Add all emission files to data directory for nested North America simulation<br />
<br />
The [[CH4_simulation#Error_reading_GWETTOP_fields|error in reading GWETTOP fields]] is also fixed in this update.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:35, 2 February 2012 (EST)<br />
<br />
=== Update CH4 emissions to EDGAR v4.2 ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02m|v9-02m]] and approved on 30 Jul 2013.'''''<br />
<br />
Kevin Wecht has prepared EDGAR v4.2 emissions of methane for 2004-2008. The data files are available at:<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/CH4_201305/<br />
<br />
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.<br />
<br />
Modifications to subroutines <tt>RICE_EMIS</tt> and <tt>ASEASONAL_ANTHRO_EMIS</tt> in <tt>global_ch4_mod.F</tt> include changing the directory names and updating CYEAR and XTAU as follows:<br />
<br />
WRITE( CYEAR, '(i4)' ) GET_YEAR()<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
<br />
IF ( GET_YEAR() .LT. 2004 ) THEN<br />
CYEAR='2004'<br />
XTAU = GET_TAU0( 1, 1, 2004 )<br />
ENDIF<br />
IF ( GET_YEAR() .GT. 2008 ) THEN<br />
CYEAR='2008'<br />
XTAU = GET_TAU0( 1, 1, 2008 )<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:53, 2 July 2013 (EDT)<br />
<br />
=== Fixes for wetland emissions ===<br />
<br />
'''''These issues were resolved during the [[GEOS-Chem_v9-02#Period_of_public_comment|public comment period]] following the provisional release of GEOS-Chem v9-02 and will be included in the official release of [[GEOS-Chem v9-02]].'''''<br />
<br />
'''''[mailto:kevin.wecht@gmail.com Kevin Wecht]''''' wrote:<br />
<br />
:I have some updates/bug fixes to wetland emissions in the methane simulation. Both changes impact global_ch4_mod.F, subroutine WETLAND_EMIS.<br />
<br />
::1. Christopher Pickett-Heaps added a feature that zeroes wetland emissions if snow covers the ground. This was never incorporated into the standard code. It is included in the attached file.<br />
<br />
::2. Parameters in the subroutine are not correct. The following values are the correct and are included in the attached file:<br />
MOIST_SCALE = 0.205<br />
EMIT_FACT = 0.018<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 16:11, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
== Previous issues that are now resolved ==<br />
<br />
=== Error reading GWETTOP fields ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
There is a file read error in the current CH4 simulation. We will fix this issue in [[GEOS-Chem v9-01-03]].<br />
<br />
In RICE_EMIS (global_ch4_mod.F), XTAU is reset to the wrong value when GEWTTOP is read. Kevin Wecht provided a fix that accounts for different availabilities of GEOS-4 and GEOS-5 met fields. Prior to setting FILENAME for GWETTOP , add the following:<br />
<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2009 ) YEAR = 2009<br />
#elif defined( GEOS_4 )<br />
IF ( YEAR .LT. 2000 ) YEAR = 2000<br />
IF ( YEAR .GT. 2006 ) YEAR = 2006<br />
#endif<br />
WRITE( CYEAR, '(i4)' ) YEAR<br />
<br />
:Also change:<br />
<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, GET_YEAR() )<br />
<br />
:to:<br />
<br />
XTAU = GET_TAU0( 1, 1, YEAR )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, YEAR )<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 18:06, 2 February 2012 (EST)<br />
<br />
== Outstanding Issues ==<br />
<br />
None reported so far.<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 30 March 2012 (EDT)</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=CH4_simulation&diff=15630CH4 simulation2014-01-24T15:27:26Z<p>Alex Turner: /* CH4 simulation user groups */</p>
<hr />
<div>This page contains information about the methane (CH4) simulation in GEOS-Chem.<br />
<br />
== Overview ==<br />
<br />
The CH4 simulation in GEOS-Chem ...<br />
<br />
=== Authors and collaborators ===<br />
* [mailto:maasakkers@fas.harvard.edu Bram Maasakkers] ''(Harvard)''<br />
* [mailto:aturner@fas.harvard.edu Alex Turner] ''(Harvard)''<br />
* [mailto:kevin.wecht@gmail.com Kevin Wecht] ''(Harvard)''<br />
* Christopher Pickett-Heaps ''(formerly @ Harvard)''<br />
* Jerome Drevet ''(formerly @ EPFL)''<br />
* James Wang ''(formerly @ Harvard)''<br />
<br />
=== CH4 simulation user groups ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group<br />
!Personnel<br />
!Projects<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/ Harvard University]<br />
|[mailto:maasakkers@fas.harvard.edu Bram Maasakkers]<br>[mailto:aturner@fas.harvard.edu Alex Turner]<br>[mailto:kevin.wecht@gmail.com Kevin Wecht]<br />
|North American methane sources (Top-Down/Bottom-Up)<br> <br />
|-valign="top"<br />
|U. Wollongong<br />
|[mailto:cm700@uow.edu.au Chris Chan Miller]<br />
|Methane sources in tropical Australia<br />
<br />
|}<br />
<br />
== Validation ==<br />
<br />
== Planned updates ==<br />
<br />
=== Update methane emissions and add capability for North America nested grid ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
'''''[mailto:wecht@fas.harvard.edu Kevin Wecht] wrote:'''''<br />
<br />
:I have some GEOS-Chem methane updates that I'd like to add to the standard code. <br />
<br />
:#GFED emissions - I've updated GFED-2 and GFED-3 biomass burning to include methane emissions.<br />
:#Methane simulation - I've updated emissions and error catches to make the simulation compatible with the nested simulation over North America. I added linearized CH4 chemistry from GMI output (CH4 loss frequencies generated by Lee Murray). These changes should be made to the data directory:<br />
<br />
:::a. Replace Carbon_soil, Carbon_litter, and Wetfrac files in data directory (for all horizontal resolutions)<br />
:::b. Add 2010-2011 TSKIN and GWETTOP files to data directory (for all horizontal resolutions)<br />
:::c. Add nested north american OH files to OH directory<br />
:::d. Add biofuel emissions to data directory (for all horizontal resolutions)<br />
:::e. Add all emission files to data directory for nested North America simulation<br />
<br />
The [[CH4_simulation#Error_reading_GWETTOP_fields|error in reading GWETTOP fields]] is also fixed in this update.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:35, 2 February 2012 (EST)<br />
<br />
=== Update CH4 emissions to EDGAR v4.2 ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02m|v9-02m]] and approved on 30 Jul 2013.'''''<br />
<br />
Kevin Wecht has prepared EDGAR v4.2 emissions of methane for 2004-2008. The data files are available at:<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/CH4_201305/<br />
<br />
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.<br />
<br />
Modifications to subroutines <tt>RICE_EMIS</tt> and <tt>ASEASONAL_ANTHRO_EMIS</tt> in <tt>global_ch4_mod.F</tt> include changing the directory names and updating CYEAR and XTAU as follows:<br />
<br />
WRITE( CYEAR, '(i4)' ) GET_YEAR()<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
<br />
IF ( GET_YEAR() .LT. 2004 ) THEN<br />
CYEAR='2004'<br />
XTAU = GET_TAU0( 1, 1, 2004 )<br />
ENDIF<br />
IF ( GET_YEAR() .GT. 2008 ) THEN<br />
CYEAR='2008'<br />
XTAU = GET_TAU0( 1, 1, 2008 )<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:53, 2 July 2013 (EDT)<br />
<br />
=== Fixes for wetland emissions ===<br />
<br />
'''''These issues were resolved during the [[GEOS-Chem_v9-02#Period_of_public_comment|public comment period]] following the provisional release of GEOS-Chem v9-02 and will be included in the official release of [[GEOS-Chem v9-02]].'''''<br />
<br />
'''''[mailto:kevin.wecht@gmail.com Kevin Wecht]''''' wrote:<br />
<br />
:I have some updates/bug fixes to wetland emissions in the methane simulation. Both changes impact global_ch4_mod.F, subroutine WETLAND_EMIS.<br />
<br />
::1. Christopher Pickett-Heaps added a feature that zeroes wetland emissions if snow covers the ground. This was never incorporated into the standard code. It is included in the attached file.<br />
<br />
::2. Parameters in the subroutine are not correct. The following values are the correct and are included in the attached file:<br />
MOIST_SCALE = 0.205<br />
EMIT_FACT = 0.018<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 16:11, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
== Previous issues that are now resolved ==<br />
<br />
=== Error reading GWETTOP fields ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
There is a file read error in the current CH4 simulation. We will fix this issue in [[GEOS-Chem v9-01-03]].<br />
<br />
In RICE_EMIS (global_ch4_mod.F), XTAU is reset to the wrong value when GEWTTOP is read. Kevin Wecht provided a fix that accounts for different availabilities of GEOS-4 and GEOS-5 met fields. Prior to setting FILENAME for GWETTOP , add the following:<br />
<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2009 ) YEAR = 2009<br />
#elif defined( GEOS_4 )<br />
IF ( YEAR .LT. 2000 ) YEAR = 2000<br />
IF ( YEAR .GT. 2006 ) YEAR = 2006<br />
#endif<br />
WRITE( CYEAR, '(i4)' ) YEAR<br />
<br />
:Also change:<br />
<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, GET_YEAR() )<br />
<br />
:to:<br />
<br />
XTAU = GET_TAU0( 1, 1, YEAR )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, YEAR )<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 18:06, 2 February 2012 (EST)<br />
<br />
== Outstanding Issues ==<br />
<br />
None reported so far.<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 30 March 2012 (EDT)</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=CH4_simulation&diff=15629CH4 simulation2014-01-24T15:27:00Z<p>Alex Turner: /* CH4 simulation user groups */</p>
<hr />
<div>This page contains information about the methane (CH4) simulation in GEOS-Chem.<br />
<br />
== Overview ==<br />
<br />
The CH4 simulation in GEOS-Chem ...<br />
<br />
=== Authors and collaborators ===<br />
* [mailto:maasakkers@fas.harvard.edu Bram Maasakkers] ''(Harvard)''<br />
* [mailto:aturner@fas.harvard.edu Alex Turner] ''(Harvard)''<br />
* [mailto:kevin.wecht@gmail.com Kevin Wecht] ''(Harvard)''<br />
* Christopher Pickett-Heaps ''(formerly @ Harvard)''<br />
* Jerome Drevet ''(formerly @ EPFL)''<br />
* James Wang ''(formerly @ Harvard)''<br />
<br />
=== CH4 simulation user groups ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group<br />
!Personnel<br />
!Projects<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/ Harvard University]<br />
|[mailto:maasakkers@fas.harvard.edu Bram Maasakkers]<br>[mailto:aturner@fas.harvard.edu Alex Turner]<br>[mailto:kevin.wecht@gmail.com Kevin Wecht]<br />
|Top-Down/Bottom-Up estimation of North American Methane sources<br> <br />
|-valign="top"<br />
|U. Wollongong<br />
|[mailto:cm700@uow.edu.au Chris Chan Miller]<br />
|Methane sources in tropical Australia<br />
<br />
|}<br />
<br />
== Validation ==<br />
<br />
== Planned updates ==<br />
<br />
=== Update methane emissions and add capability for North America nested grid ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
'''''[mailto:wecht@fas.harvard.edu Kevin Wecht] wrote:'''''<br />
<br />
:I have some GEOS-Chem methane updates that I'd like to add to the standard code. <br />
<br />
:#GFED emissions - I've updated GFED-2 and GFED-3 biomass burning to include methane emissions.<br />
:#Methane simulation - I've updated emissions and error catches to make the simulation compatible with the nested simulation over North America. I added linearized CH4 chemistry from GMI output (CH4 loss frequencies generated by Lee Murray). These changes should be made to the data directory:<br />
<br />
:::a. Replace Carbon_soil, Carbon_litter, and Wetfrac files in data directory (for all horizontal resolutions)<br />
:::b. Add 2010-2011 TSKIN and GWETTOP files to data directory (for all horizontal resolutions)<br />
:::c. Add nested north american OH files to OH directory<br />
:::d. Add biofuel emissions to data directory (for all horizontal resolutions)<br />
:::e. Add all emission files to data directory for nested North America simulation<br />
<br />
The [[CH4_simulation#Error_reading_GWETTOP_fields|error in reading GWETTOP fields]] is also fixed in this update.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:35, 2 February 2012 (EST)<br />
<br />
=== Update CH4 emissions to EDGAR v4.2 ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02m|v9-02m]] and approved on 30 Jul 2013.'''''<br />
<br />
Kevin Wecht has prepared EDGAR v4.2 emissions of methane for 2004-2008. The data files are available at:<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/CH4_201305/<br />
<br />
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.<br />
<br />
Modifications to subroutines <tt>RICE_EMIS</tt> and <tt>ASEASONAL_ANTHRO_EMIS</tt> in <tt>global_ch4_mod.F</tt> include changing the directory names and updating CYEAR and XTAU as follows:<br />
<br />
WRITE( CYEAR, '(i4)' ) GET_YEAR()<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
<br />
IF ( GET_YEAR() .LT. 2004 ) THEN<br />
CYEAR='2004'<br />
XTAU = GET_TAU0( 1, 1, 2004 )<br />
ENDIF<br />
IF ( GET_YEAR() .GT. 2008 ) THEN<br />
CYEAR='2008'<br />
XTAU = GET_TAU0( 1, 1, 2008 )<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:53, 2 July 2013 (EDT)<br />
<br />
=== Fixes for wetland emissions ===<br />
<br />
'''''These issues were resolved during the [[GEOS-Chem_v9-02#Period_of_public_comment|public comment period]] following the provisional release of GEOS-Chem v9-02 and will be included in the official release of [[GEOS-Chem v9-02]].'''''<br />
<br />
'''''[mailto:kevin.wecht@gmail.com Kevin Wecht]''''' wrote:<br />
<br />
:I have some updates/bug fixes to wetland emissions in the methane simulation. Both changes impact global_ch4_mod.F, subroutine WETLAND_EMIS.<br />
<br />
::1. Christopher Pickett-Heaps added a feature that zeroes wetland emissions if snow covers the ground. This was never incorporated into the standard code. It is included in the attached file.<br />
<br />
::2. Parameters in the subroutine are not correct. The following values are the correct and are included in the attached file:<br />
MOIST_SCALE = 0.205<br />
EMIT_FACT = 0.018<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 16:11, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
== Previous issues that are now resolved ==<br />
<br />
=== Error reading GWETTOP fields ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
There is a file read error in the current CH4 simulation. We will fix this issue in [[GEOS-Chem v9-01-03]].<br />
<br />
In RICE_EMIS (global_ch4_mod.F), XTAU is reset to the wrong value when GEWTTOP is read. Kevin Wecht provided a fix that accounts for different availabilities of GEOS-4 and GEOS-5 met fields. Prior to setting FILENAME for GWETTOP , add the following:<br />
<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2009 ) YEAR = 2009<br />
#elif defined( GEOS_4 )<br />
IF ( YEAR .LT. 2000 ) YEAR = 2000<br />
IF ( YEAR .GT. 2006 ) YEAR = 2006<br />
#endif<br />
WRITE( CYEAR, '(i4)' ) YEAR<br />
<br />
:Also change:<br />
<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, GET_YEAR() )<br />
<br />
:to:<br />
<br />
XTAU = GET_TAU0( 1, 1, YEAR )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, YEAR )<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 18:06, 2 February 2012 (EST)<br />
<br />
== Outstanding Issues ==<br />
<br />
None reported so far.<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 30 March 2012 (EDT)</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=CH4_simulation&diff=15628CH4 simulation2014-01-24T15:24:09Z<p>Alex Turner: /* Authors and collaborators */</p>
<hr />
<div>This page contains information about the methane (CH4) simulation in GEOS-Chem.<br />
<br />
== Overview ==<br />
<br />
The CH4 simulation in GEOS-Chem ...<br />
<br />
=== Authors and collaborators ===<br />
* [mailto:maasakkers@fas.harvard.edu Bram Maasakkers] ''(Harvard)''<br />
* [mailto:aturner@fas.harvard.edu Alex Turner] ''(Harvard)''<br />
* [mailto:kevin.wecht@gmail.com Kevin Wecht] ''(Harvard)''<br />
* Christopher Pickett-Heaps ''(formerly @ Harvard)''<br />
* Jerome Drevet ''(formerly @ EPFL)''<br />
* James Wang ''(formerly @ Harvard)''<br />
<br />
=== CH4 simulation user groups ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group<br />
!Personnel<br />
!Projects<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/ Harvard University]<br />
|[mailto:cpickett@seas.harvard.edu Christopher Pickett-Heaps]<br>[mailto:kevin.wecht@gmail.com Kevin Wecht]<br />
|Methane sources in the Arctic <br />
|-valign="top"<br />
|U. Wollongong<br />
|[mailto:cm700@uow.edu.au Chris Chan Miller]<br />
|Methane sources in tropical Australia<br />
<br />
|}<br />
<br />
== Validation ==<br />
<br />
== Planned updates ==<br />
<br />
=== Update methane emissions and add capability for North America nested grid ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
'''''[mailto:wecht@fas.harvard.edu Kevin Wecht] wrote:'''''<br />
<br />
:I have some GEOS-Chem methane updates that I'd like to add to the standard code. <br />
<br />
:#GFED emissions - I've updated GFED-2 and GFED-3 biomass burning to include methane emissions.<br />
:#Methane simulation - I've updated emissions and error catches to make the simulation compatible with the nested simulation over North America. I added linearized CH4 chemistry from GMI output (CH4 loss frequencies generated by Lee Murray). These changes should be made to the data directory:<br />
<br />
:::a. Replace Carbon_soil, Carbon_litter, and Wetfrac files in data directory (for all horizontal resolutions)<br />
:::b. Add 2010-2011 TSKIN and GWETTOP files to data directory (for all horizontal resolutions)<br />
:::c. Add nested north american OH files to OH directory<br />
:::d. Add biofuel emissions to data directory (for all horizontal resolutions)<br />
:::e. Add all emission files to data directory for nested North America simulation<br />
<br />
The [[CH4_simulation#Error_reading_GWETTOP_fields|error in reading GWETTOP fields]] is also fixed in this update.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:35, 2 February 2012 (EST)<br />
<br />
=== Update CH4 emissions to EDGAR v4.2 ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02m|v9-02m]] and approved on 30 Jul 2013.'''''<br />
<br />
Kevin Wecht has prepared EDGAR v4.2 emissions of methane for 2004-2008. The data files are available at:<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/CH4_201305/<br />
<br />
ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/CH4_201305/<br />
<br />
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.<br />
<br />
Modifications to subroutines <tt>RICE_EMIS</tt> and <tt>ASEASONAL_ANTHRO_EMIS</tt> in <tt>global_ch4_mod.F</tt> include changing the directory names and updating CYEAR and XTAU as follows:<br />
<br />
WRITE( CYEAR, '(i4)' ) GET_YEAR()<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
<br />
IF ( GET_YEAR() .LT. 2004 ) THEN<br />
CYEAR='2004'<br />
XTAU = GET_TAU0( 1, 1, 2004 )<br />
ENDIF<br />
IF ( GET_YEAR() .GT. 2008 ) THEN<br />
CYEAR='2008'<br />
XTAU = GET_TAU0( 1, 1, 2008 )<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:53, 2 July 2013 (EDT)<br />
<br />
=== Fixes for wetland emissions ===<br />
<br />
'''''These issues were resolved during the [[GEOS-Chem_v9-02#Period_of_public_comment|public comment period]] following the provisional release of GEOS-Chem v9-02 and will be included in the official release of [[GEOS-Chem v9-02]].'''''<br />
<br />
'''''[mailto:kevin.wecht@gmail.com Kevin Wecht]''''' wrote:<br />
<br />
:I have some updates/bug fixes to wetland emissions in the methane simulation. Both changes impact global_ch4_mod.F, subroutine WETLAND_EMIS.<br />
<br />
::1. Christopher Pickett-Heaps added a feature that zeroes wetland emissions if snow covers the ground. This was never incorporated into the standard code. It is included in the attached file.<br />
<br />
::2. Parameters in the subroutine are not correct. The following values are the correct and are included in the attached file:<br />
MOIST_SCALE = 0.205<br />
EMIT_FACT = 0.018<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 16:11, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
== Previous issues that are now resolved ==<br />
<br />
=== Error reading GWETTOP fields ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''<br />
<br />
There is a file read error in the current CH4 simulation. We will fix this issue in [[GEOS-Chem v9-01-03]].<br />
<br />
In RICE_EMIS (global_ch4_mod.F), XTAU is reset to the wrong value when GEWTTOP is read. Kevin Wecht provided a fix that accounts for different availabilities of GEOS-4 and GEOS-5 met fields. Prior to setting FILENAME for GWETTOP , add the following:<br />
<br />
YEAR = GET_YEAR()<br />
#if defined( GEOS_5 )<br />
IF ( YEAR .LT. 2004 ) YEAR = 2004<br />
IF ( YEAR .GT. 2009 ) YEAR = 2009<br />
#elif defined( GEOS_4 )<br />
IF ( YEAR .LT. 2000 ) YEAR = 2000<br />
IF ( YEAR .GT. 2006 ) YEAR = 2006<br />
#endif<br />
WRITE( CYEAR, '(i4)' ) YEAR<br />
<br />
:Also change:<br />
<br />
XTAU = GET_TAU0( 1, 1, GET_YEAR() )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, GET_YEAR() )<br />
<br />
:to:<br />
<br />
XTAU = GET_TAU0( 1, 1, YEAR )<br />
and<br />
XTAU = GET_TAU0( GET_MONTH(), 1, YEAR )<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 18:06, 2 February 2012 (EST)<br />
<br />
== Outstanding Issues ==<br />
<br />
None reported so far.<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 30 March 2012 (EDT)</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_Adjoint&diff=12999GEOS-Chem Adjoint2013-05-02T13:14:05Z<p>Alex Turner: /* Current GEOS-Chem Adjoint Research Projects (please add yours!) */</p>
<hr />
<div><big><big><strong>Adjoint and Data Assimilation Working Group</strong></big></big><br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-<br />
|'''Adjoint Working Group Co-Chairs'''<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman] and [mailto:dbj@atmosp.physics.utoronto.ca Dylan Jones]<br />
|-<br />
|-<br />
|'''Adjoint Model Scientist'''<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|'''GC adjoint support team'''<br />
|[mailto:yanko.davila@colorado.edu Yanko Davila], [mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez]<br />
|-<br />
|'''Adjoint Working Group email list'''<br />
|<tt>geos-chem-adjoint@seas.harvard.edu</tt><br />
|-<br />
|'''To subscribe to email list'''<br />
|Send email to [mailto:geos-chem-adjoint-join@seas.harvard.edu <tt>geos-chem-adjoint-join@seas.harvard.edu</tt>]<br />
|-<br />
|'''To unsubscribe from email list'''<br />
|Send email to [mailto:geos-chem-adjoint-leave@seas.harvard.edu <tt>geos-chem-adjoint-leave@seas.harvard.edu</tt>]<br />
|}<br />
<br />
== Historical Development ==<br />
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. <br />
<br />
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.<br />
<br />
== Forward Model Code ==<br />
<br />
The forward model on which the adjoint is based originally corresponded to GEOS-Chem v8-02-01. It was subsequently updated as follows:<br />
<br />
* KPP solver for gas-phase chemistry (as in GCv8-02-03)<br />
* Implement Bond 2007 BC/OC emissions (as in GCv8-02-02)<br />
* Apply bug fixes from GCv8-02-02 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-02#Previous_issues_now_resolved_in_v8-02-02 here]<br />
* Apply bug fixes from GCv8-02-03 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-03#Previous_issues_now_resolved_in_v8-02-03 here]<br />
* Apply bug fixes from GCv8-02-04 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-04#Previous_issues_now_resolved_in_v8-02-04 here]<br />
<br />
All bug fixes and model updates were previous listed at the top of inverse_driver.f. We have now switched to documenting the code development cycle here in the wiki, see the following section. <br />
<br />
== Code Versions, Bug Fixes and Developments == <br />
<br />
=== Current GEOS-Chem adjoint version released ===<br />
*[[GEOS-Chem_Adjoint_v34]] (You will download this version when you check out.)<br />
<br />
=== Previous GEOS-Chem adjoint versions released ===<br />
*[[GEOS-Chem_Adjoint_v33]] <br />
*[[GEOS-Chem_Adjoint_v32]]<br />
*[[GEOS-Chem_Adjoint_v31]]<br />
<br />
== Summary of Main Adjoint Code Supported Features ==<br />
<br />
=== Features === <br />
* Meteorological fields<br />
** GEOS-3 <i>needs testing</i><br />
** GEOS-4<br />
** GEOS-5 <br />
* model resolution<br />
** 4 x 5<br />
** 2 x 2.5 <br />
** Nested Asia and NA<br />
* Forward model processes<br />
** convection<br />
** advection<br />
** PBL mixing<br />
** dry deposition<br />
** wet deposition<br />
** strat / trop exchange with LINOZ and new GMI strat chem (v9-01-03)<br />
** NOy up fluxes (now replaced with new GMI strat chem)<br />
** aerosols <br />
*** inorganic aerosol thermodynamics with RPMARES<br />
*** inorganic aerosol thermodynamics with ISORROPIA <i> in progress </i><br />
*** sulfate chemistry <br />
*** BC<br />
*** SOA, Dust, sea salt <i> needs doing </i><br />
*** aerosol surface area feedbacks <i> needs updating </i><br />
*** aerosol optical feedbacks <i> needs doing </i><br />
** emissions<br />
*** all standard emissions included<br />
* Simulation modes<br />
** full chemistry<br />
** tagged CO<br />
** tagged Ox <br />
** CH4<br />
** offline aerosols (for BC and dust only)<br />
** CO2<br />
* Observational Operators<br />
** MOPITT CO column<br />
** SCIAMACHY CO column<br />
** AIRS CO column<br />
** IMPROVE BC<br />
** CASTNet (NH4+) <i> needs updating </i> <br />
** GOME / SCIAMACHY NO2 column <i> needs updating </i> <br />
*** using KNMI retrieval (Henze)<br />
*** using Dalhousie retrieval (Shim)<br />
** SCIAMACHY/OMI NO2<br />
*** using Dalhousie retrieval (Bousserez, Padmanabhan)<br />
** TES NH3 <br />
** TES O3 <br />
** GOSAT CO2 <br />
** MLS O3 and TES CO2 <i> in progress </i><br />
* Control parameters<br />
** Initial Conditions scaling factors (linear or log)<br />
** Emissions scaling factors (linear or log) <br />
*** NH3, primary BC/OC, SO2: anthropogenic, natural, bioburn, biomass, ship<br />
*** NOx: soil, aircraft, anthropogenic, biofuel, bioburn<br />
*** Lightning NOx: injection height, yield <i> in progress </i><br />
*** all other gas-phase tracers: anthropogenic, biofuel, bioburn <br />
* Adjoint sensitivities<br />
** w.r.t. all implemented control parameters<br />
** w.r.t Reaction Rate Parameters <br />
** w.r.t all emissions <br />
** of AQ attainment metrics <i> needs updating </i><br />
** of spatiotemporally averaged species concentrations (e.g., arctic O3) <br />
* Other<br />
** Inverse Hessian approximation <br />
** off-diagonal covariance matrices <i> needs updating </i><br />
** 3D-Var <i> needs updating </i><br />
<br />
Features may be qualified as: <br />
* <i>needs testing</i>: an implemented feature that we haven't fully used yet<br />
* <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<br />
* <i>needs doing</i>: a feature nobody has tackled the adjoint of yet<br />
* <i>in progress</i>: a feature currently under development <br />
* <i>in pipeline</i>: a feature which has been submitted and awaiting integration into the CVS repository<br />
<br />
=== Primary code developers ===<br />
Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze<br />
<br />
=== Adjoint model lead scientist ===<br />
Daven Henze<br />
<br />
<br />
<br />
== Resources ==<br />
<br />
=== User's guide ===<br />
A user's guide v34 is available. [http://adjoint.colorado.edu/~yanko/gcadj_std/GC_adj_man.pdf User's Guide v34] <br />
<br />
Previous version v32-v33 available at [http://adjoint.colorado.edu/~daven/gcadj_std/GC_adj_man.pdf User's Guide v32]<br />
<br />
=== Code flowchart ===<br />
Meemong Lee has created a detailed flowchart of the inverse model code structure. http://adjoint.colorado.edu/~daven/gcadj_std/flowchart.pdf<br />
<br />
=== Plotting tools ===<br />
<br />
Some IDL and MATLAB routines for plotting benchmark results. http://adjoint.colorado.edu/~daven/gcadj_std/tools.tar.gz<br />
<br />
=== Background papers and presentations ===<br />
<br />
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<br />
<br />
== Distribution and Use ==<br />
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.]] <br />
<br />
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. <br />
<br />
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.<br />
<br />
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 tuned 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 comunity just send Daven Henze your [[Using_Git_with_GEOS-Chem#Sharing_your_revisions_with_others_.28and_vice_versa.29|patch]] and we'll take care of the rest.<br />
<br />
=== Quick guide to GIT === <br />
As of version 34 we started using git versioning system. We recommend first taking a look at GIT manual to get a general feel for how this tools works (e.g., [http://git-scm.com/documentation GIT Documentation] or [http://www.kernel.org/pub/software/scm/git/docs/git.html GIT Manual Page]). <br />
<br />
<br />
Useful GIT commands: <br />
<br />
Initial download:<br />
git clone ssh://git@adjoint.colorado.edu:2222/gcadj_std.git<br />
<br />
Status of project vs the current repository:<br />
git status<br />
<br />
Check difference of files (differences have colors for easy reading)<br />
git diff --word-diff=color <wildcard> [<wildcard>] <path>/foo_mod.f<br />
<br />
Checkout specific version<br />
git checkout <wildcard><br />
<br />
Replacing a file with the newest version from the repository:<br />
git checkout origin/master -- <path>/foo_mod.f<br />
<br />
Merging changes in a file: ([http://www.kernel.org/pub/software/scm/git/docs/git-merge.html Reference])<br />
git merge -m <wildcard> <br />
<br />
Comitting<br />
git commit -a<br />
<br />
Tagging a version<br />
git tag -a TAGNAME<br />
<br />
Deleting a tag<br />
git tag -d TAGNAME<br />
git push origin :refs/tags/TAGNAME<br />
<br />
Saving changes to repository<br />
git push<br />
<br />
Saving tags to repository<br />
git push --tags<br />
<br />
List the history of a file:<br />
git log -- <path>/foo_mod.f<br />
<br />
Add a file to the repository<br />
git add <file_name><br />
<br />
Delete a file from the repository<br />
git rm <file_name><br />
<br />
Determine current version<br />
git show HEAD [ | grep commit]<br />
<br />
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.<br />
git pull --rebase<br />
<br />
There are several wildcards that you can use on git for example:<br/><br />
''"origin/master"'' - Latest version on the repository <br/><br />
''"HEAD"'' - Latest version as of your last download <br/><br />
''"[http://adjoint.colorado.edu:8080/gcadj_std/commits/72773d7b1a7bd757957d2c186acb3dbb107d5323 v33i]"'' - Specific TAG, find all tag names on GitLab<br/><br />
''"[http://adjoint.colorado.edu:8080/gcadj_std/commits/32d5c926ef529c1dfc640c9dec4a925b24db575c 32d5c926e]"'' - Specific COMMIT, find all commit numbers on GitLab <br/><br />
<br />
[[Using_Git_with_GEOS-Chem|Here is the foward model documentation of git.]]<br />
<br />
=== Backward compatibility (CVS) === <br />
<br />
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]]<br />
<br />
== Crediting GEOS-Chem adjoint developers ==<br />
<br />
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. <br />
<br />
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:<br />
* (v32) MOPITT v5 CO observation operator. Developer: Zhe Jiang, University of Toronto.<br />
* (v32) Dust adjoint. Developer: Xiaoguang (Richard) Xu, University of Nebraska Lincoln.<br />
* (v32) Black carbon offline aerosol adjoint. Developer: Yuhao Mao (UCLA).<br />
* (v32) Nested full chemistry adjoint. Developers: Zhe Jiang, University of Toronto; Daven Henze, CU Boulder.<br />
* (v32) Stratospheric production / loss rate sensitivities. Developer: Hyungmin Lee, CU Boulder.<br />
* (v32) CH4 adjoint. Developer: Kevin Wecht, Harvard University<br />
* (v29) LIDORT. Developer: Daven Henze, University of Colorado Boulder. Collaborator: Rob Spurr. <br />
* (v28) CO2 adjoint. Developer: Daven Henze, University of Colorado Boulder. Collaborators: Ray Nassar, Kevin Bowman, Dylan Jones.<br />
<br />
Citation of the appropriate [[GEOS-Chem_Adjoint#Journal_Articles|journal articles]] for mature developments is also encouraged, as well as considering aspects of [http://acmg.seas.harvard.edu/geos/geos_credit.html co-authorship for the forward model]. <br />
<br />
Overall, if you have any questions about authorship, even for a conference presentation, please contact Daven Henze.<br />
<br />
== Current GEOS-Chem Adjoint Research Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group <br />
!Description <br />
!Contact Person<br />
|-<br />
|CU Boulder<br />
|Aerosol precursors, CO2, O3; general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|CU Boulder<br />
|Inverse modeling/optimization; CO2 fluxes inversion (CMS project); general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Nicolas Bousserez]<br />
|-<br />
|CU Boulder<br />
|Sensitivity of nitrate deposition over Antarctica including stratospheric tracers<br />
|[mailto:hyungmin.lee@colorado.edu Hyung-Min Lee]<br />
|-<br />
|Harvard<br />
|Methane<br />
|Kevin Wecht, wecht [at] fas.harvard.edu<br />
|-<br />
|Harvard<br />
|Smoke Emissions in SE Asia<br />
|Patrick Kim, kim68 [at] fas.harvard.edu<br />
|-<br />
|Harvard<br />
|Methane from GOSAT<br />
|Alex Turner, aturner [at] fas.harvard.edu<br />
|-<br />
|Purdue University<br />
|Methane (SICAMACHY, AIRS and IASI)<br />
|[mailto:tang16@purdue.edu Jinyun Tang]<br />
|-<br />
|MIT<br />
|Aircraft emissions<br />
|[mailto:jaminkoo@mit.edu Jamin Koo]<br />
|-<br />
|MIT<br />
|Air quality, aircraft emissions and sensitivities<br />
|[mailto:bvconsta@mit.edu Bogdan V. Constantin]<br />
|-<br />
|Princeton<br />
|BC sensitivities, general adjoint code development<br />
|Monika Kopacz, mkopacz [at] princeton.edu<br />
|-<br />
|Dalhousie University<br />
|Lightning NOx emissions and impact on tropical ozone using the adjoint<br />
|[mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez (now at CU-Boulder)]<br />
|-<br />
|Dalhousie University<br />
|Surface NOx emissions inversion using SCIAMACHY/OMI NO2 measurements<br />
|Akhila Padmanabhan akhila [at] dal.ca; Nicolas Bousserez [mailto:Nicolas.Bousserez@colorado.edu] (now at CU-Boulder)<br />
|-<br />
|JPL<br />
|Microwave Limb Sounder (MLS) Ozone assimilation<br />
|[mailto:meemong.lee@jpl.nasa.gov Meemong Lee]<br />
|-<br />
|JPL <br />
| TES ozone assimilation/attribution of ozone radiative forcing<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman]<br />
|-<br />
|University of Edinburgh<br />
|Quantifying the impact of boreal forest fires on tropospheric oxidants over the Atlantic<br />
|[mailto:mark.parrington@ed.ac.uk Mark Parrington]<br />
|-<br />
|US EPA<br />
|Integration with economic models for future emission inventory scenario development<br />
|[mailto:akhtar.farhan@epa.gov Farhan Akhtar]<br />
|-<br />
|Peking University<br />
|Satellite constraints on VOC emissions <br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|-<br />
|IAP.CAS<br />
|CO2 assimilation<br />
|[mailto:czh@mail.iap.ac.cn Chen]<br />
|-<br />
|Purdue University<br />
|Feedback between terrestrial ecosystem processes and atmospheric co2 signals<br />
|[mailto:zhuq@purdue.edu Qing Zhu]<br />
|-<br />
|Purdue University<br />
|Feedback between aquatic ecosystem processes and atmospheric CH4 signals<br />
|[mailto:tan80@purdue.edu Zeli Tan]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and reactive nitrogen to precursor emissions<br />
|[mailto:twalker@atmosp.physics.utoronto.ca Thomas Walker]<br />
|-<br />
|University of Toronto<br />
|Adjoint analysis for carbon monoxide <br />
|[mailto:zjiang@atmosp.physics.utoronto.ca Zhe Jiang]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and CO to precursor emissions<br />
|[mailto:cwhaley@atmosp.physics.utoronto.ca Cynthia Whaley]<br />
|-<br />
|Georgia Tech / US EPA<br />
|ISORROPIA adjoint development; NH3 assimilation; cloud droplet sensitivities<br />
|[mailto:scapps@gatech.edu Shannon Capps]<br />
|-<br />
|Peking University<br />
|Source attributions of tropospheric ozone over North China<br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|-<br />
|University of Wollongong<br />
|Sensitivity of ozone and adjoint analysis of CO over Australasia.<br />
|[mailto:rb864@uowmail.edu.au Rebecca Buchholz]<br />
|-<br />
|University of Toronto<br />
|CO2 assimilation & transport model bias estimation<br />
|[mailto:mkeller@atmosp.physics.utoronto.ca Martin Keller]<br />
|-<br />
|University of Wisconsin<br />
|CO2 assimilation and forecast & Temperature profile retrieval <br />
|[mailto:wenguang.bai@ssec.wisc.edu Wenguang Bai]<br />
|-<br />
|Dalhousie University<br />
|Sensitivity of global PM2.5-induced mortality to emissions<br />
|[mailto:colin.lee@dal.ca Colin Lee]<br />
|-<br />
|University of Leicester (UK)<br />
|Top-down estimates of Amazon isoprene emissions<br />
|[mailto:mpb14@le.ac.uk Michael Barkley]<br />
|-<br />
|Anyang University<br />
|Aerosol emission modeling in East Asia <br />
|[mailto:koo@anyang.ac.kr Youn Seo Koo]<br />
|-<br />
|Nanjing University<br />
|Inverse modeling of terrestrial ecosystem carbon flux<br />
|[mailto:hengmao.wang@gmail.com Hengmao Wang]<br />
|-<br />
|Tsinghua University<br />
|Nested-gird simulations with the adjoint model<br />
|[mailto:nany12@mails.tsinghua.edu.cn Nan Yang]<br />
|-<br />
|University of Minnesota<br />
|Inverse modeling of VOC sources based on TES and IASI measurements<br />
|[mailto:dbm@umn.edu Dylan Millet]<br />
|-<br />
|Tsinghua University<br />
|Inverse modeling of anthropogenic emissions over East Asia<br />
|[mailto:qiangzhang@tsinghua.edu.cn Qiang Zhang]<br />
|-<br />
|UCLA<br />
|Constrain black carbon emission<br />
|[mailto:qiling@atmos.ucla.edu Ling Qi]<br />
|}<br />
<br />
== Publications ==<br />
<br />
=== Journal Articles ===<br />
<br />
* '''In press or sumbitted'''<br />
<br />
**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, JGR, in press.<br />
**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, GRL, in press.<br />
**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, in press.<br />
**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, JGR, in press.<br />
**Paulot, F., D. J. Jacob and D. K. Henze, Sources and processes contributing to nitrogen deposition in biodiversity hotspots worldwide, submitted.<br />
**Singh, K., A. Sandu, Variational Chemical Data Assimilation with Approximate Adjoints, submitted. <br />
**Xu, X., J. Wang, D. K. Henze, W. Qu, M. Kopacz, Constraints on Aerosol Sources Using GEOS-Chem Adjoint and MODIS Radiances, and Evaluation with Multi-sensor (OMI, MISR) data, submitted.<br />
<br />
* '''2012'''<br />
**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. GRL Editor's highlight, Science Daily, KGNU radio interview.<br />
**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.<br />
**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.<br />
**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, online.<br />
**Paulot, F., D. K. Henze, and P. O. Wennberg, Impact of the isoprene photochemical cascade on tropical ozone, Atmos. Chem. Phys., 12, 1307-1325, online.<br />
**Singh, K. and A. Sandu, 2012: Variational chemical data assimilation with approximate adjoints. Computers and Geosciences, 40, 10-18.<br />
**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.<br />
**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.<br />
**Wang, J., X. Xu, D. K. Henze, Q. Ji, S.-C. Tsay, 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.<br />
**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, online.<br />
<br />
* '''2011'''<br />
**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.<br />
**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.<br />
**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 online.<br />
<br />
* '''2010'''<br />
**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, online.<br />
**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.<br />
**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<br />
**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<br />
<br />
* '''2009'''<br />
**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. online<br />
**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, online.<br />
**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.<br />
**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.<br />
**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.<br />
<br />
* '''2007'''<br />
**Henze, D. K., A. Hakami and J. H. Seinfeld (2007), Development of the adjoint of GEOS-Chem, Atmos. Chem. Phys., 7, 2413-2433.<br />
<br />
=== Conference proceedings === <br />
* 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<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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<br />
<br />
* 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</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_Adjoint&diff=12909GEOS-Chem Adjoint2013-04-25T04:01:14Z<p>Alex Turner: /* Current GEOS-Chem Adjoint Research Projects (please add yours!) */</p>
<hr />
<div><big><big><strong>Adjoint and Data Assimilation Working Group</strong></big></big><br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-<br />
|'''Adjoint Working Group Co-Chairs'''<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman] and [mailto:dbj@atmosp.physics.utoronto.ca Dylan Jones]<br />
|-<br />
|-<br />
|'''Adjoint Model Scientist'''<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|'''GC adjoint support team'''<br />
|[mailto:yanko.davila@colorado.edu Yanko Davila], [mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez]<br />
|-<br />
|'''Adjoint Working Group email list'''<br />
|<tt>geos-chem-adjoint@seas.harvard.edu</tt><br />
|-<br />
|'''To subscribe to email list'''<br />
|Send email to [mailto:geos-chem-adjoint-join@seas.harvard.edu <tt>geos-chem-adjoint-join@seas.harvard.edu</tt>]<br />
|-<br />
|'''To unsubscribe from email list'''<br />
|Send email to [mailto:geos-chem-adjoint-leave@seas.harvard.edu <tt>geos-chem-adjoint-leave@seas.harvard.edu</tt>]<br />
|}<br />
<br />
== Historical Development ==<br />
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. <br />
<br />
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.<br />
<br />
== Forward Model Code ==<br />
<br />
The forward model on which the adjoint is based originally corresponded to GEOS-Chem v8-02-01. It was subsequently updated as follows:<br />
<br />
* KPP solver for gas-phase chemistry (as in GCv8-02-03)<br />
* Implement Bond 2007 BC/OC emissions (as in GCv8-02-02)<br />
* Apply bug fixes from GCv8-02-02 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-02#Previous_issues_now_resolved_in_v8-02-02 here]<br />
* Apply bug fixes from GCv8-02-03 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-03#Previous_issues_now_resolved_in_v8-02-03 here]<br />
* Apply bug fixes from GCv8-02-04 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-04#Previous_issues_now_resolved_in_v8-02-04 here]<br />
<br />
All bug fixes and model updates were previous listed at the top of inverse_driver.f. We have now switched to documenting the code development cycle here in the wiki, see the following section. <br />
<br />
== Code Versions, Bug Fixes and Developments == <br />
<br />
=== Current GEOS-Chem adjoint version released ===<br />
*[[GEOS-Chem_Adjoint_v34]] (You will download this version when you check out.)<br />
<br />
=== Previous GEOS-Chem adjoint versions released ===<br />
*[[GEOS-Chem_Adjoint_v33]] <br />
*[[GEOS-Chem_Adjoint_v32]]<br />
*[[GEOS-Chem_Adjoint_v31]]<br />
<br />
== Summary of Main Adjoint Code Supported Features ==<br />
<br />
=== Features === <br />
* Meteorological fields<br />
** GEOS-3 <i>needs testing</i><br />
** GEOS-4<br />
** GEOS-5 <br />
* model resolution<br />
** 4 x 5<br />
** 2 x 2.5 <br />
** Nested Asia and NA<br />
* Forward model processes<br />
** convection<br />
** advection<br />
** PBL mixing<br />
** dry deposition<br />
** wet deposition<br />
** strat / trop exchange with LINOZ and new GMI strat chem (v9-01-03)<br />
** NOy up fluxes (now replaced with new GMI strat chem)<br />
** aerosols <br />
*** inorganic aerosol thermodynamics with RPMARES<br />
*** inorganic aerosol thermodynamics with ISORROPIA <i> in progress </i><br />
*** sulfate chemistry <br />
*** BC<br />
*** SOA, Dust, sea salt <i> needs doing </i><br />
*** aerosol surface area feedbacks <i> needs updating </i><br />
*** aerosol optical feedbacks <i> needs doing </i><br />
** emissions<br />
*** all standard emissions included<br />
* Simulation modes<br />
** full chemistry<br />
** tagged CO<br />
** tagged Ox <br />
** CH4<br />
** offline aerosols (for BC and dust only)<br />
** CO2<br />
* Observational Operators<br />
** MOPITT CO column<br />
** SCIAMACHY CO column<br />
** AIRS CO column<br />
** IMPROVE BC<br />
** CASTNet (NH4+) <i> needs updating </i> <br />
** GOME / SCIAMACHY NO2 column <i> needs updating </i> <br />
*** using KNMI retrieval (Henze)<br />
*** using Dalhousie retrieval (Shim)<br />
** SCIAMACHY/OMI NO2<br />
*** using Dalhousie retrieval (Bousserez, Padmanabhan)<br />
** TES NH3 <br />
** TES O3 <br />
** GOSAT CO2 <br />
** MLS O3 and TES CO2 <i> in progress </i><br />
* Control parameters<br />
** Initial Conditions scaling factors (linear or log)<br />
** Emissions scaling factors (linear or log) <br />
*** NH3, primary BC/OC, SO2: anthropogenic, natural, bioburn, biomass, ship<br />
*** NOx: soil, aircraft, anthropogenic, biofuel, bioburn<br />
*** Lightning NOx: injection height, yield <i> in progress </i><br />
*** all other gas-phase tracers: anthropogenic, biofuel, bioburn <br />
* Adjoint sensitivities<br />
** w.r.t. all implemented control parameters<br />
** w.r.t Reaction Rate Parameters <br />
** w.r.t all emissions <br />
** of AQ attainment metrics <i> needs updating </i><br />
** of spatiotemporally averaged species concentrations (e.g., arctic O3) <br />
* Other<br />
** Inverse Hessian approximation <br />
** off-diagonal covariance matrices <i> needs updating </i><br />
** 3D-Var <i> needs updating </i><br />
<br />
Features may be qualified as: <br />
* <i>needs testing</i>: an implemented feature that we haven't fully used yet<br />
* <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<br />
* <i>needs doing</i>: a feature nobody has tackled the adjoint of yet<br />
* <i>in progress</i>: a feature currently under development <br />
* <i>in pipeline</i>: a feature which has been submitted and awaiting integration into the CVS repository<br />
<br />
=== Primary code developers ===<br />
Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze<br />
<br />
=== Adjoint model lead scientist ===<br />
Daven Henze<br />
<br />
<br />
<br />
== Resources ==<br />
<br />
=== User's guide ===<br />
A user's guide v34 is available. [http://adjoint.colorado.edu/~yanko/gcadj_std/GC_adj_man.pdf User's Guide v34] <br />
<br />
Previous version v32-v33 available at [http://adjoint.colorado.edu/~daven/gcadj_std/GC_adj_man.pdf User's Guide v32]<br />
<br />
=== Code flowchart ===<br />
Meemong Lee has created a detailed flowchart of the inverse model code structure. http://adjoint.colorado.edu/~daven/gcadj_std/flowchart.pdf<br />
<br />
=== Plotting tools ===<br />
<br />
Some IDL and MATLAB routines for plotting benchmark results. http://adjoint.colorado.edu/~daven/gcadj_std/tools.tar.gz<br />
<br />
=== Background papers and presentations ===<br />
<br />
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<br />
<br />
== Distribution and Use ==<br />
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.]] <br />
<br />
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. <br />
<br />
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.<br />
<br />
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 tuned 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 comunity just send Daven Henze your [[Using_Git_with_GEOS-Chem#Sharing_your_revisions_with_others_.28and_vice_versa.29|patch]] and we'll take care of the rest.<br />
<br />
=== Quick guide to GIT === <br />
As of version 34 we started using git versioning system. We recommend first taking a look at GIT manual to get a general feel for how this tools works (e.g., [http://git-scm.com/documentation GIT Documentation] or [http://www.kernel.org/pub/software/scm/git/docs/git.html GIT Manual Page]). <br />
<br />
<br />
Useful GIT commands: <br />
<br />
Initial download:<br />
git clone ssh://git@adjoint.colorado.edu:2222/gcadj_std.git<br />
<br />
Status of project vs the current repository:<br />
git status<br />
<br />
Check difference of files (differences have colors for easy reading)<br />
git diff --word-diff=color <wildcard> [<wildcard>] <path>/foo_mod.f<br />
<br />
Checkout specific version<br />
git checkout <wildcard><br />
<br />
Replacing a file with the newest version from the repository:<br />
git checkout origin/master -- <path>/foo_mod.f<br />
<br />
Merging changes in a file: ([http://www.kernel.org/pub/software/scm/git/docs/git-merge.html Reference])<br />
git merge -m <wildcard> <br />
<br />
Comitting<br />
git commit -a<br />
<br />
Tagging a version<br />
git tag -a TAGNAME<br />
<br />
Deleting a tag<br />
git tag -d TAGNAME<br />
git push origin :refs/tags/TAGNAME<br />
<br />
Saving changes to repository<br />
git push<br />
<br />
Saving tags to repository<br />
git push --tags<br />
<br />
List the history of a file:<br />
git log -- <path>/foo_mod.f<br />
<br />
Add a file to the repository<br />
git add <file_name><br />
<br />
Delete a file from the repository<br />
git rm <file_name><br />
<br />
Determine current version<br />
git show HEAD [ | grep commit]<br />
<br />
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.<br />
git pull --rebase<br />
<br />
There are several wildcards that you can use on git for example:<br/><br />
''"origin/master"'' - Latest version on the repository <br/><br />
''"HEAD"'' - Latest version as of your last download <br/><br />
''"[http://adjoint.colorado.edu:8080/gcadj_std/commits/72773d7b1a7bd757957d2c186acb3dbb107d5323 v33i]"'' - Specific TAG, find all tag names on GitLab<br/><br />
''"[http://adjoint.colorado.edu:8080/gcadj_std/commits/32d5c926ef529c1dfc640c9dec4a925b24db575c 32d5c926e]"'' - Specific COMMIT, find all commit numbers on GitLab <br/><br />
<br />
[[Using_Git_with_GEOS-Chem|Here is the foward model documentation of git.]]<br />
<br />
=== Backward compatibility (CVS) === <br />
<br />
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]]<br />
<br />
== Crediting GEOS-Chem adjoint developers ==<br />
<br />
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. <br />
<br />
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:<br />
* (v32) MOPITT v5 CO observation operator. Developer: Zhe Jiang, University of Toronto.<br />
* (v32) Dust adjoint. Developer: Xiaoguang (Richard) Xu, University of Nebraska Lincoln.<br />
* (v32) Black carbon offline aerosol adjoint. Developer: Yuhao Mao (UCLA).<br />
* (v32) Nested full chemistry adjoint. Developers: Zhe Jiang, University of Toronto; Daven Henze, CU Boulder.<br />
* (v32) Stratospheric production / loss rate sensitivities. Developer: Hyungmin Lee, CU Boulder.<br />
* (v32) CH4 adjoint. Developer: Kevin Wecht, Harvard University<br />
* (v29) LIDORT. Developer: Daven Henze, University of Colorado Boulder. Collaborator: Rob Spurr. <br />
* (v28) CO2 adjoint. Developer: Daven Henze, University of Colorado Boulder. Collaborators: Ray Nassar, Kevin Bowman, Dylan Jones.<br />
<br />
Citation of the appropriate [[GEOS-Chem_Adjoint#Journal_Articles|journal articles]] for mature developments is also encouraged, as well as considering aspects of [http://acmg.seas.harvard.edu/geos/geos_credit.html co-authorship for the forward model]. <br />
<br />
Overall, if you have any questions about authorship, even for a conference presentation, please contact Daven Henze.<br />
<br />
== Current GEOS-Chem Adjoint Research Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group <br />
!Description <br />
!Contact Person<br />
|-<br />
|CU Boulder<br />
|Aerosol precursors, CO2, O3; general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|CU Boulder<br />
|Inverse modeling/optimization; CO2 fluxes inversion (CMS project); general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Nicolas Bousserez]<br />
|-<br />
|CU Boulder<br />
|Sensitivity of nitrate deposition over Antarctica including stratospheric tracers<br />
|[mailto:hyungmin.lee@colorado.edu Hyung-Min Lee]<br />
|-<br />
|Harvard<br />
|Methane<br />
|Kevin Wecht, wecht [at] fas.harvard.edu<br />
|-<br />
|Harvard<br />
|Smoke Emissions in SE Asia<br />
|Patrick Kim, kim68 [at] fas.harvard.edu<br />
|-<br />
|Harvard<br />
|Methane<br />
|Alex Turner, aturner [at] fas.harvard.edu<br />
|-<br />
|Purdue University<br />
|Methane (SICAMACHY, AIRS and IASI)<br />
|[mailto:tang16@purdue.edu Jinyun Tang]<br />
|-<br />
|MIT<br />
|Aircraft emissions<br />
|[mailto:jaminkoo@mit.edu Jamin Koo]<br />
|-<br />
|MIT<br />
|Air quality, aircraft emissions and sensitivities<br />
|[mailto:bvconsta@mit.edu Bogdan V. Constantin]<br />
|-<br />
|Princeton<br />
|BC sensitivities, general adjoint code development<br />
|Monika Kopacz, mkopacz [at] princeton.edu<br />
|-<br />
|Dalhousie University<br />
|Lightning NOx emissions and impact on tropical ozone using the adjoint<br />
|[mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez (now at CU-Boulder)]<br />
|-<br />
|Dalhousie University<br />
|Surface NOx emissions inversion using SCIAMACHY/OMI NO2 measurements<br />
|Akhila Padmanabhan akhila [at] dal.ca; Nicolas Bousserez [mailto:Nicolas.Bousserez@colorado.edu] (now at CU-Boulder)<br />
|-<br />
|JPL<br />
|Microwave Limb Sounder (MLS) Ozone assimilation<br />
|[mailto:meemong.lee@jpl.nasa.gov Meemong Lee]<br />
|-<br />
|JPL <br />
| TES ozone assimilation/attribution of ozone radiative forcing<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman]<br />
|-<br />
|University of Edinburgh<br />
|Quantifying the impact of boreal forest fires on tropospheric oxidants over the Atlantic<br />
|[mailto:mark.parrington@ed.ac.uk Mark Parrington]<br />
|-<br />
|US EPA<br />
|Integration with economic models for future emission inventory scenario development<br />
|[mailto:akhtar.farhan@epa.gov Farhan Akhtar]<br />
|-<br />
|Peking University<br />
|Satellite constraints on VOC emissions <br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|-<br />
|IAP.CAS<br />
|CO2 assimilation<br />
|[mailto:czh@mail.iap.ac.cn Chen]<br />
|-<br />
|Purdue University<br />
|Feedback between terrestrial ecosystem processes and atmospheric co2 signals<br />
|[mailto:zhuq@purdue.edu Qing Zhu]<br />
|-<br />
|Purdue University<br />
|Feedback between aquatic ecosystem processes and atmospheric CH4 signals<br />
|[mailto:tan80@purdue.edu Zeli Tan]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and reactive nitrogen to precursor emissions<br />
|[mailto:twalker@atmosp.physics.utoronto.ca Thomas Walker]<br />
|-<br />
|University of Toronto<br />
|Adjoint analysis for carbon monoxide <br />
|[mailto:zjiang@atmosp.physics.utoronto.ca Zhe Jiang]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and CO to precursor emissions<br />
|[mailto:cwhaley@atmosp.physics.utoronto.ca Cynthia Whaley]<br />
|-<br />
|Georgia Tech / US EPA<br />
|ISORROPIA adjoint development; NH3 assimilation; cloud droplet sensitivities<br />
|[mailto:scapps@gatech.edu Shannon Capps]<br />
|-<br />
|Peking University<br />
|Source attributions of tropospheric ozone over North China<br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|-<br />
|University of Wollongong<br />
|Sensitivity of ozone and adjoint analysis of CO over Australasia.<br />
|[mailto:rb864@uowmail.edu.au Rebecca Buchholz]<br />
|-<br />
|University of Toronto<br />
|CO2 assimilation & transport model bias estimation<br />
|[mailto:mkeller@atmosp.physics.utoronto.ca Martin Keller]<br />
|-<br />
|University of Wisconsin<br />
|CO2 assimilation and forecast & Temperature profile retrieval <br />
|[mailto:wenguang.bai@ssec.wisc.edu Wenguang Bai]<br />
|-<br />
|Dalhousie University<br />
|Sensitivity of global PM2.5-induced mortality to emissions<br />
|[mailto:colin.lee@dal.ca Colin Lee]<br />
|-<br />
|University of Leicester (UK)<br />
|Top-down estimates of Amazon isoprene emissions<br />
|[mailto:mpb14@le.ac.uk Michael Barkley]<br />
|-<br />
|Anyang University<br />
|Aerosol emission modeling in East Asia <br />
|[mailto:koo@anyang.ac.kr Youn Seo Koo]<br />
|-<br />
|Nanjing University<br />
|Inverse modeling of terrestrial ecosystem carbon flux<br />
|[mailto:hengmao.wang@gmail.com Hengmao Wang]<br />
|-<br />
|Tsinghua University<br />
|Nested-gird simulations with the adjoint model<br />
|[mailto:nany12@mails.tsinghua.edu.cn Nan Yang]<br />
|-<br />
|University of Minnesota<br />
|Inverse modeling of VOC sources based on TES and IASI measurements<br />
|[mailto:dbm@umn.edu Dylan Millet]<br />
|-<br />
|Tsinghua University<br />
|Inverse modeling of anthropogenic emissions over East Asia<br />
|[mailto:qiangzhang@tsinghua.edu.cn Qiang Zhang]<br />
|-<br />
|UCLA<br />
|Constrain black carbon emission<br />
|[mailto:qiling@atmos.ucla.edu Ling Qi]<br />
|}<br />
<br />
== Publications ==<br />
<br />
=== Journal Articles ===<br />
<br />
* '''In press or sumbitted'''<br />
<br />
**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, JGR, in press.<br />
**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, GRL, in press.<br />
**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, in press.<br />
**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, JGR, in press.<br />
**Paulot, F., D. J. Jacob and D. K. Henze, Sources and processes contributing to nitrogen deposition in biodiversity hotspots worldwide, submitted.<br />
**Singh, K., A. Sandu, Variational Chemical Data Assimilation with Approximate Adjoints, submitted. <br />
**Xu, X., J. Wang, D. K. Henze, W. Qu, M. Kopacz, Constraints on Aerosol Sources Using GEOS-Chem Adjoint and MODIS Radiances, and Evaluation with Multi-sensor (OMI, MISR) data, submitted.<br />
<br />
* '''2012'''<br />
**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. GRL Editor's highlight, Science Daily, KGNU radio interview.<br />
**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.<br />
**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.<br />
**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, online.<br />
**Paulot, F., D. K. Henze, and P. O. Wennberg, Impact of the isoprene photochemical cascade on tropical ozone, Atmos. Chem. Phys., 12, 1307-1325, online.<br />
**Singh, K. and A. Sandu, 2012: Variational chemical data assimilation with approximate adjoints. Computers and Geosciences, 40, 10-18.<br />
**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.<br />
**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.<br />
**Wang, J., X. Xu, D. K. Henze, Q. Ji, S.-C. Tsay, 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.<br />
**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, online.<br />
<br />
* '''2011'''<br />
**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.<br />
**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.<br />
**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 online.<br />
<br />
* '''2010'''<br />
**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, online.<br />
**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.<br />
**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<br />
**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<br />
<br />
* '''2009'''<br />
**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. online<br />
**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, online.<br />
**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.<br />
**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.<br />
**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.<br />
<br />
* '''2007'''<br />
**Henze, D. K., A. Hakami and J. H. Seinfeld (2007), Development of the adjoint of GEOS-Chem, Atmos. Chem. Phys., 7, 2413-2433.<br />
<br />
=== Conference proceedings === <br />
* 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<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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<br />
<br />
* 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</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_Adjoint&diff=10673GEOS-Chem Adjoint2012-06-01T15:31:39Z<p>Alex Turner: /* Journal Articles */</p>
<hr />
<div><big><big><strong>Adjoint and Data Assimilation Working Group</strong></big></big><br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-<br />
|'''Adjoint Working Group Co-Chairs'''<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman] and [mailto:dbj@atmosp.physics.utoronto.ca Dylan Jones]<br />
|-<br />
|-<br />
|'''Adjoint Model Scientist'''<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|'''Adjoint Co-Model Scientist/GC adjoint support team'''<br />
|[mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez]<br />
|-<br />
|'''Adjoint Working Group email list'''<br />
|<tt>geos-chem-adjoint@seas.harvard.edu</tt><br />
|-<br />
|'''To subscribe to email list'''<br />
|Send email to [mailto:geos-chem-adjoint-join@seas.harvard.edu <tt>geos-chem-adjoint-join@seas.harvard.edu</tt>]<br />
|-<br />
|'''To unsubscribe from email list'''<br />
|Send email to [mailto:geos-chem-adjoint-leave@seas.harvard.edu <tt>geos-chem-adjoint-leave@seas.harvard.edu</tt>]<br />
|}<br />
<br />
== Historical Development ==<br />
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. <br />
<br />
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.<br />
<br />
== Forward Model Code ==<br />
<br />
The forward model on which the adjoint is based originally corresponded to GEOS-Chem v8-02-01. It was subsequently updated as follows:<br />
<br />
* KPP solver for gas-phase chemistry (as in GCv8-02-03)<br />
* Implement Bond 2007 BC/OC emissions (as in GCv8-02-02)<br />
* Apply bug fixes from GCv8-02-02 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-02#Previous_issues_now_resolved_in_v8-02-02 here]<br />
* Apply bug fixes from GCv8-02-03 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-03#Previous_issues_now_resolved_in_v8-02-03 here]<br />
* Apply bug fixes from GCv8-02-04 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-04#Previous_issues_now_resolved_in_v8-02-04 here]<br />
<br />
All bug fixes and model updates were previous listed at the top of inverse_driver.f. We have now switched to documenting the code development cycle here in the wiki, see the following section. <br />
<br />
== Code Versions, Bug Fixes and Developments == <br />
<br />
=== Current GEOS-Chem adjoint versions under development ===<br />
[[GEOS-Chem_Adjoint_v33]]<br />
<br />
=== Previous GEOS-Chem adjoint versions released ===<br />
*[[GEOS-Chem_Adjoint_v32]]<br />
*[[GEOS-Chem_Adjoint_v31]]<br />
<br />
== Summary of Main Adjoint Code Supported Features ==<br />
<br />
=== Features === <br />
* Meteorological fields<br />
** GEOS-3 <i>needs testing</i><br />
** GEOS-4<br />
** GEOS-5 <br />
* model resolution<br />
** 4 x 5<br />
** 2 x 2.5 <br />
** Nested Asia and NA<br />
* Forward model processes<br />
** convection<br />
** advection<br />
** PBL mixing<br />
** dry deposition<br />
** wet deposition<br />
** strat / trop exchange with LINOZ and new GMI strat chem (v9-01-03)<br />
** NOy up fluxes (now replaced with new GMI strat chem)<br />
** aerosols <br />
*** inorganic aerosol thermodynamics with RPMARES<br />
*** inorganic aerosol thermodynamics with ISORROPIA <i> in progress </i><br />
*** sulfate chemistry <br />
*** BC<br />
*** SOA, Dust, sea salt <i> needs doing </i><br />
*** aerosol surface area feedbacks <i> needs updating </i><br />
*** aerosol optical feedbacks <i> needs doing </i><br />
** emissions<br />
*** all standard emissions included<br />
* Simulation modes<br />
** full chemistry<br />
** tagged CO<br />
** tagged Ox <br />
** CH4<br />
** offline aerosols (for BC and dust only)<br />
** CO2<br />
* Observational Operators<br />
** MOPITT CO column<br />
** SCIAMACHY CO column<br />
** AIRS CO column<br />
** IMPROVE BC<br />
** CASTNet (NH4+) <i> needs updating </i> <br />
** GOME / SCIAMACHY NO2 column <i> needs updating </i> <br />
*** using KNMI retrieval (Henze)<br />
*** using Dalhousie retrieval (Shim)<br />
** SCIAMACHY/OMI NO2<br />
*** using Dalhousie retrieval (Bousserez, Padmanabhan)<br />
** TES NH3 <br />
** TES O3 <br />
** GOSAT CO2 <br />
** MLS O3 and TES CO2 <i> in progress </i><br />
* Control parameters<br />
** Initial Conditions scaling factors (linear or log)<br />
** Emissions scaling factors (linear or log) <br />
*** NH3, primary BC/OC, SO2: anthropogenic, natural, bioburn, biomass, ship<br />
*** NOx: soil, aircraft, anthropogenic, biofuel, bioburn<br />
*** Lightning NOx: injection height, yield <i> in progress </i><br />
*** all other gas-phase tracers: anthropogenic, biofuel, bioburn <br />
* Adjoint sensitivities<br />
** w.r.t. all implemented control parameters<br />
** w.r.t Reaction Rate Parameters <br />
** w.r.t all emissions <br />
** of AQ attainment metrics <i> needs updating </i><br />
** of spatiotemporally averaged species concentrations (e.g., arctic O3) <br />
* Other<br />
** Inverse Hessian approximation <br />
** off-diagonal covariance matrices <i> needs updating </i><br />
** 3D-Var <i> needs updating </i><br />
<br />
Features may be qualified as: <br />
* <i>needs testing</i>: an implemented feature that we haven't fully used yet<br />
* <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<br />
* <i>needs doing</i>: a feature nobody has tackled the adjoint of yet<br />
* <i>in progress</i>: a feature currently under development <br />
* <i>in pipeline</i>: a feature which has been submitted and awaiting integration into the CVS repository<br />
<br />
=== Primary code developers ===<br />
Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze<br />
<br />
=== Adjoint model lead scientist ===<br />
Daven Henze<br />
<br />
<br />
<br />
== Resources ==<br />
<br />
=== User's guide ===<br />
A user's guide is available. http://adjoint.colorado.edu/%7Edaven/gcadj_std/GC_adj_man.pdf <br />
<br />
=== Code flowchart ===<br />
Meemong Lee has created a detailed flowchart of the inverse model code structure. http://adjoint.colorado.edu/~daven/gcadj_std/flowchart.pdf<br />
<br />
=== Plotting tools ===<br />
<br />
Some IDL and MATLAB routines for plotting benchmark results. http://adjoint.colorado.edu/~daven/gcadj_std/tools.tar.gz<br />
<br />
=== Background papers and presentations ===<br />
<br />
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<br />
<br />
== Distribution and Use ==<br />
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.<br />
<br />
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. <br />
<br />
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.<br />
<br />
=== Quick guide to CVS === <br />
We recommend first taking a look at CVS manual to get a general feel for how this tools works (e.g., http://cvsbook.red-bean.com/cvsbook.html). <br />
<br />
Below are some command commands you may use for developing code and checking the status of code updates.<br />
<br />
Obtain the latest code:<br />
<br />
cvs checkout gcadj_std<br />
<br />
<br />
Generate a list (modified_files.txt) of all the files in your local copy that differ from the current repository code:<br />
<br />
cvs -q status | grep 'Status' | grep -v 'Up-to-date' > modified_files.txt<br />
<br />
<br />
Determine the difference between your local copy of a file and the version that you originally checked out (i.e., see what you changed):<br />
<br />
cvs diff foo_mod.f<br />
<br />
Note: arguments such as a filename are optional. Without listing a specific file, cvs will run the command on all files in the current directory. <br />
<br />
<br />
Determine the difference between your local copy of the code the current version in the repository (i.e., see both what you changed, and what has changed in the repository):<br />
<br />
cvs diff -D "now" foo_mod.f<br />
<br />
<br />
Merge your local file with the current repository version<br />
<br />
cvs update foo_mod.f <br />
<br />
<br />
Obtain a fresh copy of a file in the repository (without merging)<br />
<br />
rm foo_mod.f<br />
cvs update foo_mod.f <br />
<br />
<br />
Difference between the local repository and the tagged version “TAGNAME”<br />
<br />
cvs diff -r TAGNAME (< file name > for specific file)<br />
<br />
<br />
Difference between the two tagged versions “TAGNAME1” and “TAGNAME2” in the repository (shows modified files only):<br />
<br />
cvs diff -N -c -r TAGNAME2 -r TAGNAME2 | grep "Index:" > output.txt<br />
<br />
Please do not use the commit command, which is restricted to the GCadj support team (Daven Henze and Nicolas Bousserez).<br />
<br />
== Crediting GEOS-Chem adjoint developers ==<br />
<br />
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. <br />
<br />
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:<br />
* (v32) MOPITT v5 CO observation operator. Developer: Zhe Jiang, University of Toronto.<br />
* (v32) Dust adjoint. Developer: Xiaoguang (Richard) Xu, University of Nebraska Lincoln.<br />
* (v32) Black carbon offline aerosol adjoint. Developer: Yuhao Mao (UCLA).<br />
* (v32) Nested full chemistry adjoint. Developers: Zhe Jiang, University of Toronto; Daven Henze, CU Boulder.<br />
* (v32) Stratospheric production / loss rate sensitivities. Developer: Hyungmin Lee, CU Boulder.<br />
* (v32) CH4 adjoint. Developer: Kevin Wecht, Harvard University<br />
* (v29) LIDORT. Developer: Daven Henze, University of Colorado Boulder. Collaborator: Rob Spurr. <br />
* (v28) CO2 adjoint. Developer: Daven Henze, University of Colorado Boulder. Collaborators: Ray Nassar, Kevin Bowman, Dylan Jones.<br />
<br />
Citation of the appropriate [[GEOS-Chem_Adjoint#Journal_Articles|journal articles]] for mature developments is also encouraged, as well as considering aspects of [http://acmg.seas.harvard.edu/geos/geos_credit.html co-authorship for the forward model]. <br />
<br />
Overall, if you have any questions about authorship, even for a conference presentation, please contact Daven Henze.<br />
<br />
== Current GEOS-Chem Adjoint Research Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group <br />
!Description <br />
!Contact Person<br />
|-<br />
|CU Boulder<br />
|Aerosol precursors, CO2, O3; general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|CU Boulder<br />
|Inverse modeling/optimization; general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Nicolas Bousserez]<br />
|-<br />
|Harvard<br />
|Methane<br />
|Kevin Wecht, wecht [at] fas.harvard.edu<br />
|-<br />
|Purdue University<br />
|Methane (SICAMACHY, AIRS and IASI)<br />
|[mailto:tang16@purdue.edu Jinyun Tang]<br />
|-<br />
|MIT<br />
|Aircraft emissions<br />
|[mailto:jaminkoo@mit.edu Jamin Koo]<br />
|-<br />
|Princeton<br />
|BC sensitivities, general adjoint code development<br />
|Monika Kopacz, mkopacz [at] princeton.edu<br />
|-<br />
|Dalhousie University<br />
|Lightning NOx emissions and impact on tropical ozone using the adjoint<br />
|[mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez (now at CU-Boulder)]<br />
|-<br />
|Dalhousie University<br />
|Surface NOx emissions inversion using SCIAMACHY/OMI NO2 measurements<br />
|Akhila Padmanabhan akhila [at] dal.ca; Nicolas Bousserez [mailto:Nicolas.Bousserez@colorado.edu] (now at CU-Boulder)<br />
|-<br />
|JPL<br />
|Microwave Limb Sounder (MLS) Ozone assimilation<br />
|[mailto:meemong.lee@jpl.nasa.gov Meemong Lee]<br />
|-<br />
|JPL <br />
| TES ozone assimilation/attribution of ozone radiative forcing<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman]<br />
|-<br />
|University of Edinburgh<br />
|Quantifying the impact of boreal forest fires on tropospheric oxidants over the Atlantic<br />
|[mailto:mark.parrington@ed.ac.uk Mark Parrington]<br />
|-<br />
|US EPA<br />
|Integration with economic models for future emission inventory scenario development<br />
|[mailto:akhtar.farhan@epa.gov Farhan Akhtar]<br />
|-<br />
|Peking University<br />
|Satellite constraints on VOC emissions <br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|-<br />
|CU Boulder<br />
|Spatial extent of source influences on aerosol precursor columns<br />
|[mailto:alexander.turner@colorado.edu Alex Turner]<br />
|-<br />
|IAP.CAS<br />
|CO2 assimilation<br />
|[mailto:czh@mail.iap.ac.cn Chen]<br />
|-<br />
|Purdue University<br />
|Feedback between terrestrial ecosystem processes and atmospheric co2 signals<br />
|[mailto:zhuq@purdue.edu Qing Zhu]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and reactive nitrogen to precursor emissions<br />
|[mailto:twalker@atmosp.physics.utoronto.ca Thomas Walker]<br />
|-<br />
|University of Toronto<br />
|Adjoint analysis for carbon monoxide <br />
|[mailto:zjiang@atmosp.physics.utoronto.ca Zhe Jiang]<br />
|-<br />
|Georgia Tech<br />
|ISORROPIA adjoint development; inorganic aerosol precursors<br />
|[mailto:scapps@gatech.edu Shannon Capps]<br />
|-<br />
|Peking University<br />
|Source attributions of tropospheric ozone over North China<br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|-<br />
|University of Wollongong<br />
|Sensitivity of ozone and adjoint analysis of CO over Australasia.<br />
|[mailto:rb864@uowmail.edu.au Rebecca Buchholz]<br />
|-<br />
|University of Toronto<br />
|CO2 assimilation & transport model bias estimation<br />
|[mailto:mkeller@atmosp.physics.utoronto.ca Martin Keller]<br />
|-<br />
|Dalhousie University<br />
|Sensitivity of global PM2.5-induced mortality to emissions<br />
|[mailto:colin.lee@dal.ca Colin Lee]<br />
|-<br />
|University of Leicester (UK)<br />
|Top-down estimates of Amazon isoprene emissions<br />
|[mailto:mpb14@le.ac.uk Michael Barkley]<br />
|-<br />
|Anyang University<br />
|Aerosol emission modeling in East Asia <br />
|[mailto:koo@anyang.ac.kr Youn Seo Koo]<br />
|-<br />
|Nanjing University<br />
|Inverse modeling of terrestrial ecosystem carbon flux<br />
|[mailto:hengmao.wang@gmail.com Hengmao Wang]<br />
|-<br />
|Tsinghua University<br />
|Nested-gird simulations with the adjoint model<br />
|[mailto:ny07@mails.tsinghua.edu.cn Nan Yang]<br />
|-<br />
|University of Minnesota<br />
|Inverse modeling of VOC sources based on TES and IASI measurements<br />
|[mailto:dbm@umn.edu Dylan Millet]<br />
|}<br />
<br />
== Publications ==<br />
<br />
=== Journal Articles ===<br />
*Wang, J., X. Xu, D. K. Henze, Q. Ji, S.-C. Tsay, J. Huang, Top-Down Estimate of Dust Emissions through Integration of MODIS and MISR Aerosol Retrievals with the GEOS-Chem adjoint model, submitted.<br />
<br />
*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<br />
<br />
*Bowman, K. W., and D. K. Henze, Attribution of direct ozone radiative forcing to spatially-resolved emissions, submitted.<br />
<br />
*Paulot, F., D. K. Henze, and P. O. Wennberg (2012), Impact of the isoprene photochemical cascade on tropical ozone, Atmos. Chem. Phys., 12, 1307-1325, 2012.<br />
<br />
*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, submitted.<br />
<br />
*Turner, A., D. K. Henze, R. V. Martin, and A. Hakami (2012), The spatial extent of source influences on modeled column concentrations of short-lived species, ''Geophys. Res. Lett.'', doi: 10.1029/2012GL051832, in press.<br />
<br />
*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, submitted.<br />
<br />
*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. Discuss., 11, 27887-27911.<br />
<br />
*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 (2012), Impacts of midlatitude precursor emissions and local photochemistry on ozone abundances in the Arctic, J. Geophys. Res., doi:10.1029/2011JD016370.<br />
<br />
*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.<br />
<br />
*Singh, K., A. Sandu, Variational Chemical Data Assimilation with Approximate Adjoints, submitted. <br />
<br />
*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<br />
<br />
*Kopacz, M., D. L. Mauzerall, J. Wang, E. M. Leibensperger, D. K. Henze, and K. Singh (2011), Origin and radiative forcing of black carbon transported to the Himalayas and Tibetan Plateau, Atmos. Chem. Phys., 11, 2837-2852, 2011. http://www.atmos-chem-phys.net/11/2837/2011/acp-11-2837-2011.html<br />
<br />
* 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<br />
<br />
* 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<br />
<br />
* 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.<br />
<br />
* 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<br />
<br />
* Henze, D. K., A. Hakami and J. H. Seinfeld (2007), Development of the adjoint of GEOS-Chem, Atmos. Chem. Phys., 7, 2413-2433.<br />
<br />
=== Conference proceedings === <br />
* 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<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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<br />
<br />
* 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</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_Adjoint&diff=10672GEOS-Chem Adjoint2012-06-01T15:29:19Z<p>Alex Turner: /* Current GEOS-Chem Adjoint Research Projects (please add yours!) */</p>
<hr />
<div><big><big><strong>Adjoint and Data Assimilation Working Group</strong></big></big><br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-<br />
|'''Adjoint Working Group Co-Chairs'''<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman] and [mailto:dbj@atmosp.physics.utoronto.ca Dylan Jones]<br />
|-<br />
|-<br />
|'''Adjoint Model Scientist'''<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|'''Adjoint Co-Model Scientist/GC adjoint support team'''<br />
|[mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez]<br />
|-<br />
|'''Adjoint Working Group email list'''<br />
|<tt>geos-chem-adjoint@seas.harvard.edu</tt><br />
|-<br />
|'''To subscribe to email list'''<br />
|Send email to [mailto:geos-chem-adjoint-join@seas.harvard.edu <tt>geos-chem-adjoint-join@seas.harvard.edu</tt>]<br />
|-<br />
|'''To unsubscribe from email list'''<br />
|Send email to [mailto:geos-chem-adjoint-leave@seas.harvard.edu <tt>geos-chem-adjoint-leave@seas.harvard.edu</tt>]<br />
|}<br />
<br />
== Historical Development ==<br />
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. <br />
<br />
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.<br />
<br />
== Forward Model Code ==<br />
<br />
The forward model on which the adjoint is based originally corresponded to GEOS-Chem v8-02-01. It was subsequently updated as follows:<br />
<br />
* KPP solver for gas-phase chemistry (as in GCv8-02-03)<br />
* Implement Bond 2007 BC/OC emissions (as in GCv8-02-02)<br />
* Apply bug fixes from GCv8-02-02 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-02#Previous_issues_now_resolved_in_v8-02-02 here]<br />
* Apply bug fixes from GCv8-02-03 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-03#Previous_issues_now_resolved_in_v8-02-03 here]<br />
* Apply bug fixes from GCv8-02-04 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-04#Previous_issues_now_resolved_in_v8-02-04 here]<br />
<br />
All bug fixes and model updates were previous listed at the top of inverse_driver.f. We have now switched to documenting the code development cycle here in the wiki, see the following section. <br />
<br />
== Code Versions, Bug Fixes and Developments == <br />
<br />
=== Current GEOS-Chem adjoint versions under development ===<br />
[[GEOS-Chem_Adjoint_v33]]<br />
<br />
=== Previous GEOS-Chem adjoint versions released ===<br />
*[[GEOS-Chem_Adjoint_v32]]<br />
*[[GEOS-Chem_Adjoint_v31]]<br />
<br />
== Summary of Main Adjoint Code Supported Features ==<br />
<br />
=== Features === <br />
* Meteorological fields<br />
** GEOS-3 <i>needs testing</i><br />
** GEOS-4<br />
** GEOS-5 <br />
* model resolution<br />
** 4 x 5<br />
** 2 x 2.5 <br />
** Nested Asia and NA<br />
* Forward model processes<br />
** convection<br />
** advection<br />
** PBL mixing<br />
** dry deposition<br />
** wet deposition<br />
** strat / trop exchange with LINOZ and new GMI strat chem (v9-01-03)<br />
** NOy up fluxes (now replaced with new GMI strat chem)<br />
** aerosols <br />
*** inorganic aerosol thermodynamics with RPMARES<br />
*** inorganic aerosol thermodynamics with ISORROPIA <i> in progress </i><br />
*** sulfate chemistry <br />
*** BC<br />
*** SOA, Dust, sea salt <i> needs doing </i><br />
*** aerosol surface area feedbacks <i> needs updating </i><br />
*** aerosol optical feedbacks <i> needs doing </i><br />
** emissions<br />
*** all standard emissions included<br />
* Simulation modes<br />
** full chemistry<br />
** tagged CO<br />
** tagged Ox <br />
** CH4<br />
** offline aerosols (for BC and dust only)<br />
** CO2<br />
* Observational Operators<br />
** MOPITT CO column<br />
** SCIAMACHY CO column<br />
** AIRS CO column<br />
** IMPROVE BC<br />
** CASTNet (NH4+) <i> needs updating </i> <br />
** GOME / SCIAMACHY NO2 column <i> needs updating </i> <br />
*** using KNMI retrieval (Henze)<br />
*** using Dalhousie retrieval (Shim)<br />
** SCIAMACHY/OMI NO2<br />
*** using Dalhousie retrieval (Bousserez, Padmanabhan)<br />
** TES NH3 <br />
** TES O3 <br />
** GOSAT CO2 <br />
** MLS O3 and TES CO2 <i> in progress </i><br />
* Control parameters<br />
** Initial Conditions scaling factors (linear or log)<br />
** Emissions scaling factors (linear or log) <br />
*** NH3, primary BC/OC, SO2: anthropogenic, natural, bioburn, biomass, ship<br />
*** NOx: soil, aircraft, anthropogenic, biofuel, bioburn<br />
*** Lightning NOx: injection height, yield <i> in progress </i><br />
*** all other gas-phase tracers: anthropogenic, biofuel, bioburn <br />
* Adjoint sensitivities<br />
** w.r.t. all implemented control parameters<br />
** w.r.t Reaction Rate Parameters <br />
** w.r.t all emissions <br />
** of AQ attainment metrics <i> needs updating </i><br />
** of spatiotemporally averaged species concentrations (e.g., arctic O3) <br />
* Other<br />
** Inverse Hessian approximation <br />
** off-diagonal covariance matrices <i> needs updating </i><br />
** 3D-Var <i> needs updating </i><br />
<br />
Features may be qualified as: <br />
* <i>needs testing</i>: an implemented feature that we haven't fully used yet<br />
* <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<br />
* <i>needs doing</i>: a feature nobody has tackled the adjoint of yet<br />
* <i>in progress</i>: a feature currently under development <br />
* <i>in pipeline</i>: a feature which has been submitted and awaiting integration into the CVS repository<br />
<br />
=== Primary code developers ===<br />
Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze<br />
<br />
=== Adjoint model lead scientist ===<br />
Daven Henze<br />
<br />
<br />
<br />
== Resources ==<br />
<br />
=== User's guide ===<br />
A user's guide is available. http://adjoint.colorado.edu/%7Edaven/gcadj_std/GC_adj_man.pdf <br />
<br />
=== Code flowchart ===<br />
Meemong Lee has created a detailed flowchart of the inverse model code structure. http://adjoint.colorado.edu/~daven/gcadj_std/flowchart.pdf<br />
<br />
=== Plotting tools ===<br />
<br />
Some IDL and MATLAB routines for plotting benchmark results. http://adjoint.colorado.edu/~daven/gcadj_std/tools.tar.gz<br />
<br />
=== Background papers and presentations ===<br />
<br />
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<br />
<br />
== Distribution and Use ==<br />
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.<br />
<br />
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. <br />
<br />
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.<br />
<br />
=== Quick guide to CVS === <br />
We recommend first taking a look at CVS manual to get a general feel for how this tools works (e.g., http://cvsbook.red-bean.com/cvsbook.html). <br />
<br />
Below are some command commands you may use for developing code and checking the status of code updates.<br />
<br />
Obtain the latest code:<br />
<br />
cvs checkout gcadj_std<br />
<br />
<br />
Generate a list (modified_files.txt) of all the files in your local copy that differ from the current repository code:<br />
<br />
cvs -q status | grep 'Status' | grep -v 'Up-to-date' > modified_files.txt<br />
<br />
<br />
Determine the difference between your local copy of a file and the version that you originally checked out (i.e., see what you changed):<br />
<br />
cvs diff foo_mod.f<br />
<br />
Note: arguments such as a filename are optional. Without listing a specific file, cvs will run the command on all files in the current directory. <br />
<br />
<br />
Determine the difference between your local copy of the code the current version in the repository (i.e., see both what you changed, and what has changed in the repository):<br />
<br />
cvs diff -D "now" foo_mod.f<br />
<br />
<br />
Merge your local file with the current repository version<br />
<br />
cvs update foo_mod.f <br />
<br />
<br />
Obtain a fresh copy of a file in the repository (without merging)<br />
<br />
rm foo_mod.f<br />
cvs update foo_mod.f <br />
<br />
<br />
Difference between the local repository and the tagged version “TAGNAME”<br />
<br />
cvs diff -r TAGNAME (< file name > for specific file)<br />
<br />
<br />
Difference between the two tagged versions “TAGNAME1” and “TAGNAME2” in the repository (shows modified files only):<br />
<br />
cvs diff -N -c -r TAGNAME2 -r TAGNAME2 | grep "Index:" > output.txt<br />
<br />
Please do not use the commit command, which is restricted to the GCadj support team (Daven Henze and Nicolas Bousserez).<br />
<br />
== Crediting GEOS-Chem adjoint developers ==<br />
<br />
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. <br />
<br />
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:<br />
* (v32) MOPITT v5 CO observation operator. Developer: Zhe Jiang, University of Toronto.<br />
* (v32) Dust adjoint. Developer: Xiaoguang (Richard) Xu, University of Nebraska Lincoln.<br />
* (v32) Black carbon offline aerosol adjoint. Developer: Yuhao Mao (UCLA).<br />
* (v32) Nested full chemistry adjoint. Developers: Zhe Jiang, University of Toronto; Daven Henze, CU Boulder.<br />
* (v32) Stratospheric production / loss rate sensitivities. Developer: Hyungmin Lee, CU Boulder.<br />
* (v32) CH4 adjoint. Developer: Kevin Wecht, Harvard University<br />
* (v29) LIDORT. Developer: Daven Henze, University of Colorado Boulder. Collaborator: Rob Spurr. <br />
* (v28) CO2 adjoint. Developer: Daven Henze, University of Colorado Boulder. Collaborators: Ray Nassar, Kevin Bowman, Dylan Jones.<br />
<br />
Citation of the appropriate [[GEOS-Chem_Adjoint#Journal_Articles|journal articles]] for mature developments is also encouraged, as well as considering aspects of [http://acmg.seas.harvard.edu/geos/geos_credit.html co-authorship for the forward model]. <br />
<br />
Overall, if you have any questions about authorship, even for a conference presentation, please contact Daven Henze.<br />
<br />
== Current GEOS-Chem Adjoint Research Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group <br />
!Description <br />
!Contact Person<br />
|-<br />
|CU Boulder<br />
|Aerosol precursors, CO2, O3; general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|-<br />
|CU Boulder<br />
|Inverse modeling/optimization; general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Nicolas Bousserez]<br />
|-<br />
|Harvard<br />
|Methane<br />
|Kevin Wecht, wecht [at] fas.harvard.edu<br />
|-<br />
|Purdue University<br />
|Methane (SICAMACHY, AIRS and IASI)<br />
|[mailto:tang16@purdue.edu Jinyun Tang]<br />
|-<br />
|MIT<br />
|Aircraft emissions<br />
|[mailto:jaminkoo@mit.edu Jamin Koo]<br />
|-<br />
|Princeton<br />
|BC sensitivities, general adjoint code development<br />
|Monika Kopacz, mkopacz [at] princeton.edu<br />
|-<br />
|Dalhousie University<br />
|Lightning NOx emissions and impact on tropical ozone using the adjoint<br />
|[mailto:Nicolas.Bousserez@colorado.edu Nicolas Bousserez (now at CU-Boulder)]<br />
|-<br />
|Dalhousie University<br />
|Surface NOx emissions inversion using SCIAMACHY/OMI NO2 measurements<br />
|Akhila Padmanabhan akhila [at] dal.ca; Nicolas Bousserez [mailto:Nicolas.Bousserez@colorado.edu] (now at CU-Boulder)<br />
|-<br />
|JPL<br />
|Microwave Limb Sounder (MLS) Ozone assimilation<br />
|[mailto:meemong.lee@jpl.nasa.gov Meemong Lee]<br />
|-<br />
|JPL <br />
| TES ozone assimilation/attribution of ozone radiative forcing<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman]<br />
|-<br />
|University of Edinburgh<br />
|Quantifying the impact of boreal forest fires on tropospheric oxidants over the Atlantic<br />
|[mailto:mark.parrington@ed.ac.uk Mark Parrington]<br />
|-<br />
|US EPA<br />
|Integration with economic models for future emission inventory scenario development<br />
|[mailto:akhtar.farhan@epa.gov Farhan Akhtar]<br />
|-<br />
|Peking University<br />
|Satellite constraints on VOC emissions <br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|-<br />
|CU Boulder<br />
|Spatial extent of source influences on aerosol precursor columns<br />
|[mailto:alexander.turner@colorado.edu Alex Turner]<br />
|-<br />
|IAP.CAS<br />
|CO2 assimilation<br />
|[mailto:czh@mail.iap.ac.cn Chen]<br />
|-<br />
|Purdue University<br />
|Feedback between terrestrial ecosystem processes and atmospheric co2 signals<br />
|[mailto:zhuq@purdue.edu Qing Zhu]<br />
|-<br />
|University of Toronto<br />
|Sensitivity of ozone and reactive nitrogen to precursor emissions<br />
|[mailto:twalker@atmosp.physics.utoronto.ca Thomas Walker]<br />
|-<br />
|University of Toronto<br />
|Adjoint analysis for carbon monoxide <br />
|[mailto:zjiang@atmosp.physics.utoronto.ca Zhe Jiang]<br />
|-<br />
|Georgia Tech<br />
|ISORROPIA adjoint development; inorganic aerosol precursors<br />
|[mailto:scapps@gatech.edu Shannon Capps]<br />
|-<br />
|Peking University<br />
|Source attributions of tropospheric ozone over North China<br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|-<br />
|University of Wollongong<br />
|Sensitivity of ozone and adjoint analysis of CO over Australasia.<br />
|[mailto:rb864@uowmail.edu.au Rebecca Buchholz]<br />
|-<br />
|University of Toronto<br />
|CO2 assimilation & transport model bias estimation<br />
|[mailto:mkeller@atmosp.physics.utoronto.ca Martin Keller]<br />
|-<br />
|Dalhousie University<br />
|Sensitivity of global PM2.5-induced mortality to emissions<br />
|[mailto:colin.lee@dal.ca Colin Lee]<br />
|-<br />
|University of Leicester (UK)<br />
|Top-down estimates of Amazon isoprene emissions<br />
|[mailto:mpb14@le.ac.uk Michael Barkley]<br />
|-<br />
|Anyang University<br />
|Aerosol emission modeling in East Asia <br />
|[mailto:koo@anyang.ac.kr Youn Seo Koo]<br />
|-<br />
|Nanjing University<br />
|Inverse modeling of terrestrial ecosystem carbon flux<br />
|[mailto:hengmao.wang@gmail.com Hengmao Wang]<br />
|-<br />
|Tsinghua University<br />
|Nested-gird simulations with the adjoint model<br />
|[mailto:ny07@mails.tsinghua.edu.cn Nan Yang]<br />
|-<br />
|University of Minnesota<br />
|Inverse modeling of VOC sources based on TES and IASI measurements<br />
|[mailto:dbm@umn.edu Dylan Millet]<br />
|}<br />
<br />
== Publications ==<br />
<br />
=== Journal Articles ===<br />
*Wang, J., X. Xu, D. K. Henze, Q. Ji, S.-C. Tsay, J. Huang, Top-Down Estimate of Dust Emissions through Integration of MODIS and MISR Aerosol Retrievals with the GEOS-Chem adjoint model, submitted.<br />
<br />
*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<br />
<br />
*Bowman, K. W., and D. K. Henze, Attribution of direct ozone radiative forcing to spatially-resolved emissions, submitted.<br />
<br />
*Paulot, F., D. K. Henze, and P. O. Wennberg (2012), Impact of the isoprene photochemical cascade on tropical ozone, Atmos. Chem. Phys., 12, 1307-1325, 2012.<br />
<br />
*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, submitted.<br />
<br />
*Turner, A., D. K. Henze, R. V. Martin, and A. Hakami, Modeled source influences on column concentrations of short-lived species, submitted.<br />
<br />
*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, submitted.<br />
<br />
*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. Discuss., 11, 27887-27911.<br />
<br />
*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 (2012), Impacts of midlatitude precursor emissions and local photochemistry on ozone abundances in the Arctic, J. Geophys. Res., doi:10.1029/2011JD016370.<br />
<br />
*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.<br />
<br />
*Singh, K., A. Sandu, Variational Chemical Data Assimilation with Approximate Adjoints, submitted. <br />
<br />
*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<br />
<br />
*Kopacz, M., D. L. Mauzerall, J. Wang, E. M. Leibensperger, D. K. Henze, and K. Singh (2011), Origin and radiative forcing of black carbon transported to the Himalayas and Tibetan Plateau, Atmos. Chem. Phys., 11, 2837-2852, 2011. http://www.atmos-chem-phys.net/11/2837/2011/acp-11-2837-2011.html<br />
<br />
* 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<br />
<br />
* 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<br />
<br />
* 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.<br />
<br />
* 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<br />
<br />
* Henze, D. K., A. Hakami and J. H. Seinfeld (2007), Development of the adjoint of GEOS-Chem, Atmos. Chem. Phys., 7, 2413-2433.<br />
<br />
=== Conference proceedings === <br />
* 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<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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<br />
<br />
* 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</div>Alex Turnerhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_Adjoint&diff=5849GEOS-Chem Adjoint2010-12-14T17:23:02Z<p>Alex Turner: /* Current GEOS-Chem Adjoint Research Projects (please add yours!) */</p>
<hr />
<div><big><big><strong>Adjoint and Data Assimilation Working Group</strong></big></big><br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-<br />
|'''Adjoint Working Group Chair'''<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman]<br />
|-<br />
|-<br />
|'''Adjoint Model Scientist'''<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|'''Adjoint Working Group email list'''<br />
|<tt>geos-chem-adjoint@seas.harvard.edu</tt><br />
|-<br />
|'''To subscribe to email list'''<br />
|Send email to [mailto:geos-chem-adjoint-join@seas.harvard.edu <tt>geos-chem-adjoint-join@seas.harvard.edu</tt>]<br />
|-<br />
|'''To unsubscribe from email list'''<br />
|Send email to [mailto:geos-chem-adjoint-leave@seas.harvard.edu <tt>geos-chem-adjoint-leave@seas.harvard.edu</tt>]<br />
|}<br />
<br />
== Historical Development ==<br />
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. <br />
<br />
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.<br />
<br />
== Current Forward Model Code ==<br />
<br />
The forward model on which the adjoint is based corresponds to GEOS-Chem v8-02-01 with the following updates:<br />
<br />
* KPP solver for gas-phase chemistry (as in GCv8-02-03)<br />
* Implement Bond 2007 BC/OC emissions (as in GCv8-02-02)<br />
* Apply bug fixes from GCv8-02-02 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-02#Previous_issues_now_resolved_in_v8-02-02 here]<br />
* Apply bug fixes from GCv8-02-03 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-03#Previous_issues_now_resolved_in_v8-02-03 here]<br />
* Apply bug fixes from GCv8-02-04 listed [http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_v8-02-04#Previous_issues_now_resolved_in_v8-02-04 here]<br />
<br />
== Current Adjoint Code ==<br />
<br />
=== Features === <br />
* Meteorological fields<br />
** GEOS-3 <i>needs testing</i><br />
** GEOS-4<br />
** GEOS-5 <br />
* model resolution<br />
** 4 x 5<br />
** 2 x 2.5 <br />
* Forward model processes<br />
** convection<br />
** advection<br />
** PBL mixing<br />
** dry deposition<br />
** wet deposition<br />
** strat / trop exchange with LINOZ <br />
** NOy up fluxes <br />
** aerosols <br />
*** inorganic aerosol thermodynamics <br />
*** sulfate chemistry <br />
*** BC<br />
*** SOA, Dust, sea salt <i> needs doing </i><br />
*** aerosol surface area feedbacks <i> needs updating </i><br />
*** aerosol optical feedbacks <i> needs doing </i><br />
** emissions<br />
*** all standard emissions included<br />
* Simulation modes<br />
** full chemistry<br />
** tagged CO<br />
** tagged Ox <br />
** CO2<br />
** methane <i> in progress </i><br />
* Observational Operators<br />
** MOPITT CO column<br />
** SCIAMACHY CO column<br />
** AIRS CO column<br />
** IMPROVE PM2.5 (NO3, SO4, OC, BC) <i> needs updating </i><br />
** CASTNet (NH4+) <i> needs updating </i> <br />
** GOME / SCIAMACHY NO2 column <i> needs updating </i> <br />
*** using KNMI retrieval (Henze)<br />
*** using Dalhousie retrieval (Shim)<br />
** TES NH3 <br />
** TES O3 <br />
** GOSAT CO2 <br />
* Control parameters<br />
** Initial Conditions scaling factors (linear or log)<br />
** Emissions scaling factors (linear or log) <br />
*** NH3, primary BC/OC, SO2: anthropogenic, natural, bioburn, biomass, ship<br />
*** NOx: soil, aircraft, anthropogenic, biofuel, bioburn<br />
*** Lightning NOx: injection height, yield <i> in progress </i><br />
*** all other gas-phase tracers: anthropogenic, biofuel, bioburn <br />
* Adjoint sensitivities<br />
** w.r.t. all implemented control parameters<br />
** w.r.t Reaction Rate Parameters <br />
** w.r.t all emissions <br />
** of AQ attainment metrics <i> needs updating </i><br />
** of spatiotemporally averaged species concentrations (e.g., arctic O3) <br />
* Other<br />
** Inverse Hessian approximation <i> needs updating </i><br />
** off-diagonal covariance matrices <i> needs updating </i><br />
** 3D-Var <i> needs updating </i><br />
<br />
Features may be qualified as: <br />
* <i>needs testing</i>: an implemented feature that we haven't fully used yet<br />
* <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<br />
* <i>needs doing</i>: a feature nobody has tackled the adjoint of yet<br />
<br />
=== Primary code developers ===<br />
Monika Kopacz, Kumaresh Singh, Changsub Shim, Daven Henze<br />
<br />
=== Adjoint model lead scientist ===<br />
Daven Henze <br />
<br />
== Documentation ==<br />
<br />
=== User's guide ===<br />
A user's guide is available. http://adjoint.colorado.edu/%7Edaven/gcadj_std/GC_adj_man.pdf <br />
<br />
=== Code flowchart ===<br />
Meemong Lee has created a detailed flowchart of the inverse model code structure. http://adjoint.colorado.edu/~daven/gcadj_std/flowchart.pdf<br />
<br />
== Distribution and Use ==<br />
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.<br />
<br />
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. <br />
<br />
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. <br />
<br />
== Giving credit for using the adjoint model ==<br />
<br />
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. <br />
<br />
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. <br />
<br />
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. <br />
<br />
Overall, if you have any questions about authorship, even for a conference presentation, please contact Daven Henze. <br />
<br />
<br />
== Current GEOS-Chem Adjoint Research Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group <br />
!Description <br />
!Contact Person<br />
|-<br />
|CU Boulder<br />
|Aerosol precursors, CO2, O3; general adjoint code maintenance<br />
|[mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|Harvard<br />
|Methane<br />
|[mailto:wecht@fas.harvard.edu Kevin Wecht]<br />
|-<br />
|Purdue University<br />
|Methane (SICAMACHY, AIRS and IASI)<br />
|[mailto:tang16@purdue.edu Jinyun Tang]<br />
|-<br />
|MIT<br />
|Aircraft emissions<br />
|[mailto:jaminkoo@mit.edu Jamin Koo]<br />
|-<br />
|Princeton<br />
|BC sensitivities, general adjoint code development<br />
|Monika Kopacz, mkopacz [at] princeton.edu<br />
|-<br />
|Dalhousie University<br />
|Lightning NOx emissions and impact on tropical ozone using the adjoint<br />
|[mailto:N.Bousserez@dal.ca Nicolas Bousserez]<br />
|-<br />
|JPL<br />
|Microwave Limb Sounder (MLS) Ozone assimilation<br />
|[mailto:meemong.lee@jpl.nasa.gov Meemong Lee]<br />
|-<br />
|JPL <br />
| TES ozone assimilation/attribution of ozone radiative forcing<br />
|[mailto:kevin.bowman@jpl.nasa.gov Kevin Bowman]<br />
|-<br />
|University of Edinburgh<br />
|Quantifying the impact of boreal forest fires on tropospheric oxidants over the Atlantic<br />
|[mailto:mark.parrington@ed.ac.uk Mark Parrington]<br />
|-<br />
|US EPA<br />
|Integration with economic models for future emission inventory scenario development<br />
|[mailto:akhtar.farhan@epa.gov Farhan Akhtar]<br />
|-<br />
|Peking University<br />
|Satellite constraints on VOC emissions <br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|-<br />
|CU Boulder<br />
|Aerosol precursor emissions<br />
|[mailto:alexander.turner@colorado.edu Alex Turner]<br />
|-<br />
|}<br />
<br />
== Get Involved ==<br />
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). <br />
<br />
Kevin Bowman organizes bimonthly conference calls concerning current adjoint model activities.<br />
<br />
<br />
== Publications ==<br />
<br />
=== Journal Articles ===<br />
*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<br />
<br />
*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<br />
<br />
* 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<br />
<br />
* 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<br />
<br />
* 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.<br />
<br />
* 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<br />
<br />
* Henze, D. K., A. Hakami and J. H. Seinfeld (2007), Development of the adjoint of GEOS-Chem, Atmos. Chem. Phys., 7, 2413-2433.<br />
<br />
<br />
=== Conference proceedings === <br />
* 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<br />
<br />
* 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.<br />
<br />
* 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.<br />
<br />
* 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.</div>Alex Turner