Lightning NOx emissions

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GEOS-Chem v11-02-final will also carry the designation GEOS-Chem 12.0.0. We are migrating to a purely numeric versioning system in order to adhere more closely to software development best practices. For a complete description of the new versioning system, please see our GEOS-Chem version numbering system wiki page.




On this page we list various updates to GEOS-Chem's lightning NOx emissions algorithm.

Generating OTD/LIS factors

When running a GEOS-Chem simulation for a time period that doesn't have OTS/LIS factors, your simulation will stop with the following error:

    Your model framework has not had its
    lightnox code reprocessed for the correction
    to how CLDTOPS are calculated, probably due to
    the lack of your met fields at Harvard.
    
    Please contact Lee Murray
    (ltmurray@post.harvard.edu), who can help you
    prepare the necessary modifications and files
    to get lightnox working for you.
    
    You may remove this trap in lightnox_nox_mod.f
    at your own peril, but be aware that the
    magnitude and distribution of lightnox may be
    unrealistic.
    
    You can explicitly set the beta value in your
    HEMCO configuration file by adding it to the
    'Lightning NOx settings:
    # ExtNr ExtName            on/off Species
    103     LightNOx         : on     NO
        --> OTD-LIS scaling  :        1.00e-3
        
      CALL HCO_ERROR( 'Wrong beta - see information in standard output', RC )

To guarantee that lightning remains reasonable during your simulation period, you'll need to provide Lee Murray with the unconstrained flash rates so he can generate the OTD/LIS factor.

To generate unconstrained flash rates, run GEOS-Chem for your full period and turn off all emissions except lightning in HEMCO_Config.rc:

103     LightNOx          : on    NO
    --> OTD-LIS factors   :       false
    --> OTD-LIS scaling   :       1.000001
    --> CDF table         :       $ROOT/LIGHTNOX/v2014-07/light_dist.ott2010.dat

To speed up the simulation, we also recommend disabling all processes (transport, chemistry, convection, wet deposition, dry deposition) in input.geos. To avoid hitting the above error in this simulation, you can either use OTD-LIS scaling : 1.000001 in HEMCO_Config.rc or manually comment out the IF ( BETA == 1d0 ) trap in HEMCO/Extensions/hcox_lightnox_mod.F90 (you will need to inform Lee of which method you used). Archive monthly mean lightning flash rates using the ND56 diagnostic and send those to Lee Murray.

--Melissa Sulprizio (talk) 16:15, 18 November 2016 (UTC)

OTD/LIS redistribution for GEOS-FP

OTD/LIS factors in GEOS-Chem v10-01

In GEOS-Chem v10-01 and newer versions, the OTD/LIS lightning redistribution factors are read with the HEMCO emissions component. We have created new OTD/LIS data files (in COARDS-compliant netCDF format) for use with HEMCO. These new data files are contained in the HEMCO data directory tree. For detailed instructions on how to download these data files to your disk server, please see our Downloading the HEMCO data directories wiki post.

--Bob Y. 16:31, 13 February 2015 (EST)

OTD/LIS factors in GEOS-Chem v9-02

Lee Murray has generated OTD-LIS local redistribution factors for use with the GEOS-FP met fields. The scale factors were based on GEOS-FP met data from April 2012 through September 2013.

You may obtain the new OTD/LIS scale factors from:

ftp ftp.as.harvard.edu
cd gcgrid/data/GEOS_4x5/lightning_NOx_201311
mget *
cd gcgrid/data/GEOS_2x2.5/lightning_NOx_201311
mget *
cd gcgrid/data/GEOS_0.5x0.666_NA/lightning_NOx_201311
mget *
cd gcgrid/data/GEOS_0.25x0.3125_NA/lightning_NOx_201311
mget *

The OTD/LIS files are named with the following convention:

OTD-LIS-Local-Redist.CTH.v5.geos5.*
OTD-LIS-Local-Redist.CTH.v5.geosfp.*

Note that the version of the data has been updated from v4 to v5, in order to distinguish them from the files in the previous directory lightning_NOx_201101/.

Code updates have also been made to lightning_nox_mod.f in GEOS-Chem v9-02, so that GEOS-Chem reads in these new OTD/LIS local factors.

--Bob Y. 13:13, 18 June 2014 (EDT)

Update OTD/LIS factors for GEOS-FP through October 2014

These updates were validated with the 1-month benchmark simulation v10-01h and approved on Approved 01 May 2015.

Lee Murray has generated OTD-LIS factors for GEOS-FP through October 2014. These updates will be brought into GEOS-Chem v10-01 via HEMCO.

Users of GEOS-Chem v9-02 may use the updated OTD/LIS factors by following the steps below.

Download the updated OTD/LIS scale factors

You may obtain the latest OTD/LIS scale factors using:

ftp ftp.as.harvard.edu
cd gcgrid/data/GEOS_4x5/lightning_NOx_201408
mget *
cd gcgrid/data/GEOS_2x2.5/lightning_NOx_201408
mget *
cd gcgrid/data/GEOS_0.25x0.3125_NA/lightning_NOx_201408
mget *

Modify the code in lightning_nox_mod.F

(1) In routine READ_LOCAL_REDIST, change FILENAME to point to the lightning_NOx_201408 data directory and use the appropriate suffix. The code should now look like this:

      ! OTD-LIS local redist filename for CTH parameterization
      ! Now read from lightning_NOx_201408 (ltm, 7/23/14)
      FILENAME = 
     &        'lightning_NOx_201408/OTD-LIS-Local-Redist.CTH.v5.' // 
     &        TRIM( MODELNAME ) // '.' // GET_RES_EXT()

      ! Prefix directory to file name
      FILENAME = TRIM( DATA_DIR ) // TRIM( FILENAME ) 

      ! Append suffix for GEOS-FP nested grids
#if   defined( GEOS_FP ) && defined( NESTED_CH )
      FILENAME = TRIM( FILENAME ) // '.CH'
#elif defined( GEOS_FP ) && defined( NESTED_NA )
      FILENAME = TRIM( FILENAME ) // '.NA'
#elif defined( GEOS_FP ) && defined( NESTED_EU ) 
      FILENAME = TRIM( FILENAME ) // '.EU'
#elif defined( GEOS_FP ) && defined( NESTED_SE ) 
      FILENAME = TRIM( FILENAME ) // '.SE'
#endif

      ! Append suffix for developmental lightning redistribution files
      ! This file constrains lightning distribution from Apr. 2012-Oct. 2014
      ! (ltm, 12/10/2014)
#if   defined( GEOS_FP )
      FILENAME = TRIM( FILENAME ) // '.v20141210'
#endif

(2) In routine READ_LOCAL_REDIST, update the BETA factors for GEOS-FP. The code should now look like this:

#if   defined( GEOS_FP ) && defined( GRID4x5 ) 

      !---------------------------------------
      ! GEOS-FP: 4 x 5 global simulation
      !---------------------------------------

      ! Constrained with simulated "climatology" for
      ! April 2012 - Oct 2014. Will need to be updated as more
      ! met fields become available (ltm, 2014-12-10).
      IF ( ( GET_YEAR() .eq. 2012 .and. GET_MONTH() .ge. 4  ) .or.
     &     ( GET_YEAR() .eq. 2013                           ) .or.
     &     ( GET_YEAR() .eq. 2014 .and. GET_MONTH() .le. 10 ) ) THEN
         BETA = ANN_AVG_FLASHRATE / 82.373293d0
      ENDIF

#elif defined( GEOS_FP ) && defined( GRID2x25 )

      !---------------------------------------
      ! GEOS-FP: 2 x 2.5 global simulation
      !---------------------------------------
 
      ! Constrained with simulated "climatology" for
      ! April 2012 - Oct 2014. Will need to be updated as more
      ! met fields become available (ltm, 2014-12-10).
      IF ( ( GET_YEAR() .eq. 2012 .and. GET_MONTH() .ge. 4  ) .or.
     &     ( GET_YEAR() .eq. 2013                           ) .or.
     &     ( GET_YEAR() .eq. 2014 .and. GET_MONTH() .le. 10 ) ) THEN
         BETA = ANN_AVG_FLASHRATE / 260.40253d0
      ENDIF

#elif defined( GEOS_FP ) && defined( GRID025x0325 ) && defined( NESTED_CH )

      !---------------------------------------
      ! GEOS-FP: Nested China simulation
      !---------------------------------------
     
      ! Constrained with simulated "climatology" for
      ! Jan 2013 - Dec 2013. Will need to be updated as more
      ! met fields become available (ltm, 2014-10-22).
      IF ( ( cYr .eq. 2013 .and. cMt .ge. 1  )   .or. &
           ( cYr .eq. 2013 .and. cMt .le. 12 ) ) THEN
         BETA = ANN_AVG_FLASHRATE / 1052.6366d0
      ENDIF

#elif defined( GEOS_FP ) && defined( GRID025x03125 ) && defined( NESTED_NA )

      !---------------------------------------
      ! GEOS-FP: Nested N America simulation
      !---------------------------------------

      ! Constrained with simulated "climatology" for
      ! April 2012 - Oct 2014. Will need to be updated as more
      ! met fields become available (ltm, 2015-01-13).
      IF ( ( GET_YEAR() .eq. 2012 .and. GET_MONTH() .ge. 4  ) .or. 
     &     ( GET_YEAR() .eq. 2013                           ) .or.
     &     ( GET_YEAR() .eq. 2014 .and. GET_MONTH() .le. 10 ) ) THEN
         BETA = ANN_AVG_FLASHRATE / 720.10258d0
      ENDIF

(3) In routine INIT_LIGHTNING_NOX, change FILENAME to point to the lightning_NOx_201408 data directory.

     !=================================================================
     ! Read lightning CDF from Ott et al [JGR, 2010]. (ltm, 1/25/11)
     !=================================================================

     ! Define filename
     FILENAME = 'lightning_NOx_201408/light_dist.ott2010.dat'
     FILENAME = TRIM( DATA_DIR ) // TRIM( FILENAME ) 

--Melissa Sulprizio 14:19, 12 January 2015 (EST)

OTD/LIS redistribution for MERRA 2x2.5

This update was tested in the 1-month benchmark simulation v9-01-03g and approved on 27 Feb 2012.

Matt Cooper wrote:

I've been working with Lee Murray on scaling the lightning NOx for use with MERRA at 2x2.5. I've attached the new lightning_nox_mod that Lee made that now includes a scaling factor for MERRA. I've tested it and it produces the expected flash rates and lightning NOx amounts. So this is ready to included in the model.

--Melissa Payer 15:29, 22 February 2012 (EST)

Previous issues that are now resolved

Update WEST_NS_DIV to fix ozone overestimate in southern US

This update was validated with 1-month benchmark simulation v11-01f and 1-year benchmark simulation v11-01k-Run0. This version was approved on 19 Dec 2016.

From Travis et al. (2016, ACP):

We constrain the lightning NOx source with satellite data as described by Murray et al. (2012). Lightning NOx is mainly released at the top of convective updrafts following Ott et al. (2010). The standard GEOS-Chem model uses higher NOx yields for midlatitudes lightning (500 mol flash-1) than for tropical (260 mol flash-1) (Huntrieser et al. 2007, 2008; Hudman et al., 2007; Ott et al., 2010) with a fairly arbitrary boundary between the two at 23° N in North America and 35° N in Eurasia. Zhang et al. (2014) previously found that this leads GEOS-Chem to overestimate background ozone in the southwestern US and we find the same here for the eastern US and the Gulf of Mexico. We treat here all lightning in the 35° S-35° N band as tropical and this remove the distinction between North America and Eurasia.

Katie Travis wrote:

All that is needed [for this update] is to change the following line in hcox_lightnox_mod.F90 from
 REAL*8,  PARAMETER            :: WEST_NS_DIV   =  23d0
to
 REAL*8,  PARAMETER            :: WEST_NS_DIV   =  35d0

--Melissa Sulprizio (talk) 20:57, 2 December 2016 (UTC)

Obsolete information

These sections pertain to code or data that has been removed from the most recent versions of GEOS-Chem. We shall keep this information here for reference.

OTD/LIS redistribution for GEOS-5

Obsolete.jpg

OTD/LIS factors in GEOS-Chem v10-01 via HEMCO

In GEOS-Chem v10-01 and newer versions, the OTD/LIS lightning redistribution factors are read with the HEMCO emissions component. We have created new OTD/LIS data files (in COARDS-compliant netCDF format) for use with HEMCO. These new data files are contained in the HEMCO data directory tree. For detailed instructions on how to download these data files to your disk server, please see our Downloading the HEMCO data directories wiki post.

--Bob Y. 13:16, 3 March 2015 (EST)

Correct problem in OTD-LIS local redistribution files

Obsolete.jpg

This fix was validated with the 1-month benchmark simulation v11-01c and approved on 14 Sept 2015.

Christoph Keller wrote:

Lu and I just figured out that there might be a problem with the lightning NOx OTD-LIS local redistribution files for GEOS-5 simulations: the two files (OTD-LIS-Local-Redist.CTH.v5.geos5.1.0.4x5.nc and OTD-LIS-Local-Redist.CTH.v5.geos5.2.0.4x5.nc) should be merged into one single file and we should then refer to this file in the HEMCO configuration file, e.g.:
  103 LIGHTNOX_OTDLIS $ROOT/LIGHTNOX/v2014-07/OTD-LIS-Local-Redist.CTH.v5.{LNOX}.$RES.nc OTD $YYYY/1-12/1/0 C xy unitless NO - 1 1
Should evaluate to
  103 LIGHTNOX_OTDLIS $ROOT/LIGHTNOX/v2014-07/OTD-LIS-Local-Redist.CTH.v5.geos5.4x5.nc OTD $YYYY/1-12/1/0 C xy unitless NO - 1 1
The problem with the monthly GEOS-5 redistribution factors is that they change from version 5.1.0 to 5.2.0, with the switch occurring on September 2008. My solution to this problem was to create one single file that covers years 2007 to 2009. The monthly data of 2007 is then the full year of 5.1.0 data, and year 2009 covers the entire 5.2.0 data. Year 2008 is a hybrid with 5.1.0 data from Jan – Aug and 5.2.0 fields afterwards. HEMCO will then automatically pick the correct scale factors depending on the current simulation year!

--Melissa Sulprizio (talk) 17:07, 3 August 2015 (UTC)

OTD/LIS factors in GEOS-Chem v9-02 and earlier versions

Obsolete.jpg

Updated OTD/LIS local redistribution for GEOS-5

Lee Murray has regenerated the OTD/LIS local redistribution factors for use with the new reprocessed GEOS-5 met data fields. The scale factors were based on GEOS-5 met data from Dec 2003 through Feb 2009.

IMPORTANT! It is important to download the reprocessed GEOS-5 met data as soon as possible. This reprocessed data eliminates the optical depth error that was previously noted some months ago. The GEOS-5 reprocessing effort was concluded on July 10, 2009.

You may obtain the new OTD/LIS scale factors from:

ftp ftp.as.harvard.edu
cd pub/geos-chem/data/GEOS_4x5/lightning_NOx_200907
mget *
cd pub/geos-chem/data/GEOS_2x2.5/lightning_NOx_200907
mget *
cd pub/geos-chem/data/GEOS_0.5x0.666_CH/lightning_NOx_200907
mget *

The OTD/LIS files are named with the following convention:

OTD-LIS-Local-Redist.CTH.v4.geos4.*
OTD-LIS-Local-Redist.CTH.v4.geos5.*

Note that the version of the data has been updated from v3 to v4, in order to distinguish them from the files in the previous directory lightning_NOx_200709/.

NOTE: The GEOS-4 files in lightning_NOx_200907/ are identical to those in lightning_NOx_200709/. For consistency and simplicity of coding, they have been renamed from v3 to v4.

You will also need to get an updated version of source code file lightning_nox_mod.f, which has been modified to read in these new OTD/LIS local factors. You may obtain this from:

ftp ftp.as.harvard.edu
cd /lustre/pub/ftp/pub/geos-chem/patches/v8-02-02

NOTE: You must also compile GEOS-Chem with the

#define IN_CLOUD_OD 'IN_CLOUD_OD'

switch activated in the define.h header file. However, at a later time the IN_CLOUD_OD switch will be removed from the code. We will keep it for now in case some GEOS-Chem users may not have all of the GEOS-5 met data downloaded onto their systems.

--Bob Y. 10:00, 4 February 2010 (EST)

17-Jul-2008

Obsolete.jpg

Clarification: the method described by Lee Murray below expands upon previous work as described by Sauvage et al., ACP 2007.

--Bob Y. 16:14, 17 July 2008 (EDT)

22-Apr-2008

Obsolete.jpg

It was discovered that GEOS-5 lighting was consistently lower than in GEOS-4:

Lee Murray wrote:

HERE is a ppt on the lightning problem in GEOS5.
The punch line is that the horizontal distribution of lightning in GEOS5 v8-01-01 is smaller than GEOS4, and more importantly the climatology, so local redistribution was causing a net loss in lightning flashes (~11%), and mostly over Central Asia which appeared to affect the N MidLat background (North America emissions match GEOS4 very well). I am currently implementing the fix that I propose in the last slide, which preliminary results seem to indicate eradication of the problem.
Please let me know if you have any questions/concerns.
~Lee

Daniel Jacob replied:

Hi Lee - thanks for the analysis! A problem I have with waiving the CTH requirement is that if we emit lightning from shallow clouds it's like not having lightning at all - the NOx will have a short lifetime and little effect. I prefer increasing the mid-latitudes yield per flash in order to have the right amount injected in the UT at northern mid-latitudes. I understand your concern about the yield per flash already being at the upper end of literature values. But increasing the yield is just a computational convenience - what we would effectively be doing in fact is displacing the flashes to neighboring regions where the model does have deep convection, and we would do it in a simple way rather than having a complicated algorithm to search for neighboring gridboxes. Let me know what you think. Daniel

Therefore we have made the following updates for lightning in GEOS-5:

  1. We now consider lightning to be produced at cloud top heights where T > -40 C.
  2. We have created new OTD/LIS flash redistribution files for GEOS-5.

Lee Murray replied:

The totals are now brought up to realistic values (see post script).
Let me know if you have any questions.
~Lee
  ## New 4x5 LNOx totals
  Category: NOX-LI-$    Tracer:    NOx   Cum Total:       6.0708 Tg N
  --------------------------------------------------------------------------
  TAU0 =  175320.00,    NYMD = 20050101,    Total =       0.3633 Tg N
  TAU0 =  176064.00,    NYMD = 20050201,    Total =       0.3378 Tg N
  TAU0 =  176736.00,    NYMD = 20050301,    Total =       0.4205 Tg N
  TAU0 =  177480.00,    NYMD = 20050401,    Total =       0.4454 Tg N
  TAU0 =  178200.00,    NYMD = 20050501,    Total =       0.5362 Tg N
  TAU0 =  178944.00,    NYMD = 20050601,    Total =       0.6714 Tg N
  TAU0 =  179664.00,    NYMD = 20050701,    Total =       0.7286 Tg N
  TAU0 =  180408.00,    NYMD = 20050801,    Total =       0.7432 Tg N
  TAU0 =  181152.00,    NYMD = 20050901,    Total =       0.5377 Tg N
  TAU0 =  181872.00,    NYMD = 20051001,    Total =       0.4931 Tg N
  TAU0 =  182616.00,    NYMD = 20051101,    Total =       0.4212 Tg N
  TAU0 =  183336.00,    NYMD = 20051201,    Total =       0.3724 Tg N

  ## New 2x25 July and Aug LNOx totals
  Category: NOX-LI-$    Tracer:    NOx   Cum Total:       1.4678 Tg N
  --------------------------------------------------------------------------
  TAU0 =  179664.00,    NYMD = 20050701,    Total =       0.7256 Tg N
  TAU0 =  180408.00,    NYMD = 20050801,    Total =       0.7422 Tg N

--Bmy 09:50, 22 April 2008 (EDT)