Lightning NOx emissions

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Revision as of 19:22, 12 January 2015 by Melissa Payer (Talk | contribs) (Update OTD/LIS factors for GEOS-FP through October 2014)

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

OTD/LIS redistribution for GEOS-FP

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:

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:


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

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. NOTE: OTD/LIS factors for the 0.25x0.3125 NA nested grid are currently available through May 2014. The factors through October 2014 are currently being calculated and will be made available soon.

Download the updated OTD/LIS scale factors

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

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

      ! Append suffix for GEOS-FP nested grids
#if   defined( GEOS_FP ) && defined( NESTED_CH )
#elif defined( GEOS_FP ) && defined( NESTED_NA )
#elif defined( GEOS_FP ) && defined( NESTED_EU ) 
#elif defined( GEOS_FP ) && defined( NESTED_SE ) 

      ! 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'

(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, 12/10/14).
      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

#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, 12/10/14).
      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

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

      ! GEOS-FP: Nested China simulation
      ! ltm: Will need to be determined when met fields become available.

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

      ! GEOS-FP: Nested N America simulation

      ! Constrained with simulated "climatology" for
      ! April 2012 - May 2014. Will need to be updated as more
      ! met fields become available (ltm, 07/23/14).
      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 / 689.68452d0

(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_201101/light_dist.ott2010.dat'

--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)

OTD/LIS redistribution for GEOS-5

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:

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:


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:

cd /lustre/pub/ftp/pub/geos-chem/patches/v8-02-02

NOTE: You must also compile GEOS-Chem with the


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)


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)


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.

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.
  ## 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)

BETA values for North America for years after 2008

If you are using the North-American Nested-Grid simulation for years post-2008, then you should be aware of the following. We will add this update into GEOS-Chem v9-01-03.

Lee Murray wrote:

Since the operational version of GEOS5 used for the assimilation by GMAO changed in October 2008 from 5.1.0 to 5.2.0, which use different convection schemes, the lightning redistribution (i.e., satellite climatological constraint) needs to be determined for 5.2.0 separately. However, Harvard doesn't host Nested NA 2009-2010, so I couldn't generate the necessary input files until others had sent me the unconstrained lightning flash rates who had previously downloaded from the Dalhousie archive with those years. You should expect an annual average about 0.005 Tg N d-1 across the North American domain, with a summertime peak of about 0.01 Tg N d-1.
However, a few warnings. Using the attached lightning constraint will be an improvement over running unconstrained, however there are substantial interannual changes in the lightning distribution -- especially at the nested horizontal resolution. The constraint will make the 2009-2010 lightning distribution that of the 1995-2005 climatological mean, and therefore perhaps not be indicative of actual lightning in 2009 or 2010. And since only two years are used to generate a simulated climatology for comparison with the long term satellite climatology, the problem may be exacerbated.

--Bob Y. 16:07, 28 February 2012 (EST)

The common block bug fix

Lee Murray has identified a bug in the existing code (GEOS-Chem v7-04-12) which manifests itself when lightning emissions are turned off in GEOS-Chem. The bug causes non-physical values to propagate through the tracer array...this shows up as anomalous CO concentrations at high altitudes over the tropics.

Lee Murray wrote:

The bug of simply turning off lightning in input.geos in a clean build of GEOS-Chem v7-04-12 causing the CO (and other species) to explode has been fixed. (see attached)
We use common block arrays to pass lightning and aircraft (GEMISNOX) and soil (GEMISNOX2) emissions to the SMVGEAR solver. If a common block is called only in a subroutine, apparently (perhaps architecture/compiler-specific) it is able to occasionally lose its values (I had to really dig up old comments on F77 programming), which is feeding junk values into the model.
I don't know if this will correct the problems that Ray and I had with the local-rescaling lightning as well. It is quite possible that this is also common block error, though maybe not. I will continue to investigate.
The only sure way to eliminate this problem for certain is to eliminate the use of common block arrays (which is something that's been on the to-do list for a while). If we're going to be overhauling lightning for v7-04-13, I would strongly recommend that we switch over to the use of allocated arrays to hold the lightning emissions. (This would then also require modifying at least the aircraft emissions similarly).
Do you agree?

ERROR: note weird values in CO

File:Lnox common block error.png

FIXED: weird values in CO disappear

File:Lnox common block error fixed.png

Bob Yantosca replied that the preferred way to fix this error would be to replace the common block array GEMISNOX with separate module arrays for lightning NOx (EMIS_LI_NOx) and Aircraft NOx (EMIS_AC_NOx). This fix will be implemented into GEOS-Chem v7-04-13.

Bob Yantosca replied:

It's probably better to just take the GEMISNOX array out of the common block completely and to create separate module arrays for lightning and aircraft emissions. That should get rid of any instability.
Indeed, some of these common-block errors can be very esoteric. As Lee said, they may be specific to a given compiler/platform combination. Some of these types of errors may also depend on what level of optimization that you use to compile the code. Fortran optimizers can do stuff like try to force common blocks to align themselves in multiples of 64kb chunks or other weird stuff (unless you tell it not to).
We do have some common blocks still in GEOS-Chem, mainly in the legacy code and 3rd-party code sections (i.e. emissions, SMVGEAR, FAST-J, ISORROPIA, etc.). It is often difficult to totally remove all of the common blocks in the older code sections without making changes in a lot of other places as well. Newer parts of GEOS-Chem have been written to the F90 specifications.
Bob Y.

Replacing the near-land algorithm


Lee Murray (see correspondence below) has submitted a revised algorithm for lightning NOx emissions. This will be added into GEOS-Chem internal version v7-04-13.

Lee Murray wrote:

Here's a list of the changes in the lightning code over v7.04.12 that I'm about to send over to Bob for inclusion into the standard model -- these are all what I have been running my sensitivity simulations with, and I think are improvements. I just want to make sure that these sound reasonable to everyone -- please let me know if you have any concerns/objections.
  1. Elimination of "near-land" treatment -- reverting to a single "lightning_nox_mod.f" ("lightning_nox_nl_mod.f" will be removed). This offers a significant improvement in correlation with the climatology on its own.
  2. Elimination of all top-down scaling -- Attempt to have a physically-based parameterization.
  3. Elimination of emissions per path length. This relied on the grossly-simplified assumption that the relative path lengths vary as the linear ratio between the vertical distances between the negative charge layer with the ground and the cloud top heights for CG or IC flashes, respectively. The CG and IC path lengths (which have significant horizontal components and many multiple strokes per flash) almost definitely do not follow this relationship -- and we don't differentially distribute vertically anyway. In the future, we can look at aggregated pdfs of path lengths available from single-storm measurements to make a more appropriate distinction (hopefully in conjunction with different vertical pdfs). This was already done for N MIdLats, but now for tropics too.
  4. Tropical flashes at 260 mol/fl -- from Randall's constraint of 4.4 Tg N in the tropics and the OTD-LIS climatology for the region he considered. (Versus 500 mol/fl currently in the model for N MidLat, as per Rynda's work). Both of these are within the range of values in the literature. The 500 is at the upper range. The 260 is very close to the mean/median (and will be applied to ~80% of all flashes).
  5. New Local Scaling -- Now monthly rather than seasonally, since we have the high res monthly climatology and there are significant intra-seasonal spatial variability in the lightning distribution -- particularly over the SE USA. Also, set the redist factor in boxes where the model parameterization calculates no lightning over the OTD-LIS window (May 1995-Dec 2005) but OTD-LIS saw some to 1.0 (I believe Bastien set them to 0.0), so as not to suppress future years that may want to put lightning there via the param.
    (For now, have inserted a logical trap to cancel the simulation if the regional redistribution is selected. Once my study is done, then we just remove the trap in a future version)
  6. New input.geos mid-level scaling option -- If turned on (may be used with or without any of the redistributions), it will multiply every box by a uniform factor determined such that the 11-year parameterized and observed average annual flash rates (~46 flashes per second) are equal. This will be a highly recommended feature. CTH does an okay job without it, but PRECON and MFLUX really need it to be brought to the correct order of magnitude (at least in GEOS4). However, leave it optional so that one can use the unmodified physical parameterizations as well if they so choose. In the future, this may be modified to be a year-specific scaling factor as determined by the LIS observations.
  7. Recommended options in "input.geos"
  => Use lightning NOx?  : T
     => Scale glb flrate : T
     => OTD reg redist?  : F
     => OTD local redist?: T
     => Use CTH param?   : T
     => Use MFLUX param? : F
     => Use PRECON param?: F