TransportTracers simulation

This page contains information about the Radon-Lead-Beryllium simulation in GEOS-Chem.

Overview

The Rn-Pb-Be simulation in GEOS-Chem was based on that of the old Harvard/GISS CTM model. The current simulation follows Liu et al [2001].

The standard Rn-Pb-Be simulation uses the following tracers:

1. Rn²²², which is emitted naturally from soils
2. Pb²¹⁰, which is the primary decay product of Rn²²²
3. Be⁷, which is produced by cosmic rays in the stratosphere and upper atmosphere

This simulation is most frequently used to validate the convection and advection processes in GEOS-Chem.

Prior to GEOS-Chem v9-02, the Rn-Pb-Be simulation was not compatible with the non-local PBL mixing scheme. If you are running the Rn-Pb-Be simulation with any version of GEOS-Chem prior to v9-02, you must select the TURBDAY PBL mixing scheme for the Rn-Pb-Be simulation. See below for more information.

— Bob Yantosca, 28 May 2014

Sources

Species	Chemical source
Rn222	The source of Rn222 is determined as follows (cf. Jacob et al [1997]): Latitudes Rn222 Emission 90°N - 70°N Everywhere: 0.0 atoms/cm2/s 70°N - 60°N Everywhere: 0.005 atoms/cm2/s Reduce emissions by a factor of 3 where surface temperature < 0° C 60°N - 60°S Over land: 1 atom/cm2/s Over oceans: 0.005 atoms/cm2/s Reduce emissions by a factor of 3 where surface temperature < 0° C 60°S - 70°S Everywhere: 0.005 atoms/cm2/s Reduce emissions by a factor of 3 where surface temperature < 0° C 70°S - 90°S Everywhere: 0.0 atoms/cm2/s
Pb210	Radioactive decay from Rn222 according to the exponential law: EXP( -ΔT * 2.097d-6 ) Where ΔT is the emission timestep in seconds.
Be7	The source of Be7 is taken from the following reference: Lal, D., and B. Peters, Cosmic ray produced radioactivity on the Earth. Handbuch der Physik, 46/2, 551-612, edited by K. Sitte, Springer-Verlag, New York, 1967. with the following modifications (cf. Liu et al [2001]): Replace data at (0 hPa altitude, 70°S latitude) following Koch [1996]: old value = 3000 disintegrations/g air/s new value = 1900 disintegrations/g air/s The original Lal & Peters data ended at 70°S Copy the data values at 70°S to 80°S and 90°S at all levels

--Bob Y. (talk) 19:26, 15 June 2015 (UTC)

Sinks

The table below shows the sinks for Rn²²², Pb²¹⁰, and Be⁷. In the equations below, ΔT is the emission timestep in seconds.

Species	Chemical sink	Drydep sink?	Wetdep sink?
Rn222	Decays into Pb210 according to the exponential law: EXP( -ΔT * 2.097d-6 )	no	no
Pb210	Decays according to the exponential law: EXP( -ΔT * 9.725d-10 )	yes	yes
Be7	Decays according to the exponential law: EXP( -ΔT * 1.506d-7 )	yes	yes

--Bob Y. (talk) 18:48, 15 June 2015 (UTC)

Dry deposition

The following dry deposition updates were recently made to the GEOS-Chem Rn-Pb-Be simulation:

GEOS-Chem v10-01

In GEOS-Chem v10-01 and higher versions, dry deposition of advected tracers was centralized into the module GeosCore/mixing_mod.F90. This has the following implications for the GEOS-Chem Rn-Pb-Be simulation:

1. Routine DRYFLXRnPbBe—which is where dry deposition losses had been applied to Pb²¹⁰ and Be⁷ in prior GEOS-Chem versions—has now been removed from module GeosCore/drydep_mod.F. This routine has been rendered obsolete.
2. Routine DO_TEND in module GeosCore/mixing_mod.F90 now computes the ND44 diagnostic (i.e. archival of Pb²¹⁰ and Be⁷ dry deposition fluxes. This diagnostic was formerly updated in routine DRYFLXRnPbBe, which has since been removed.
3. IMPORTANT!!! GEOS-Chem v10-01 now archives the ND44 dry deposition fluxes (i.e. GAMAP category DRYD-FLX) as molec/cm2/s for ALL simulations. (In prior GEOS-Chem versions, the ND44 drydep fluxes had units of kg/s.) Therefore, when using output from the GEOS-Chem v10-01 Rn-Pb-Be simulation, make sure to adjust your data analysis programs to expect dry deposition fluxes in molec/cm2/s.
   • Also note: For the Rn-Pb-Be simulation, molec/cm2/s really means atoms/cm2/s. GEOS-Chem uses the same unit string molec/cm2/s regardless of whether a species is an element or a molecule.

--Bob Y. (talk) 20:34, 15 June 2015 (UTC)

Non-local PBL mixing

GEOS-Chem v9-02

This update was tested in the 1-month benchmark simulation v9-02o and approved on 03 Sep 2013.

Capability to use the non-local PBL mixing scheme was added in GEOS-Chem v9-02. Code updates were provided by Jintai Lin.

Karen Yu evaluated the non-local PBL mixing scheme in the Rn-Pb-Be simulation using GEOS-5 and GEOS-FP met fields. Please see these plots comparing the simulation with and without the non-local PBL mixing scheme.

--Bob Yantosca (talk) 16:43, 8 January 2016 (UTC)

GEOS-Chem v9-01-03 and earlier

Helen Amos discovered that the Rn-Pb-Be simulation was not compatible with non-local PBL mixing. In GEOS-Chem v9-01-03 and earlier, You must use the TURBDAY PBL mixing scheme. In the Chemistry Menu of input.geos:

Turn on PBL Mixing?     : T
 => Use non-local PBL?  : F

--Melissa Sulprizio 17:56, 5 August 2013 (EDT)

Validation

The information was computed from 1-year Rn-Pb-Be benchmark simulations.

1-year benchmark simulations

Benchmark plots

Version	Link
v9-01-02 w/ GEOS-5	http://wiki.seas.harvard.edu/geos-chem/index.php/Rn-Pb-Be_simulation#Comparison_plots
v9-01-03e w/ GEOS-5	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/RnPbBe/output/pdf/
v9-02r w/ GEOS-5	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-02/v9-02r/geos5/RnPbBe/output/pdf/
v9-02r w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-02/v9-02r/geosfp/RnPbBe/output/pdf/
v10-01 w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01-public-release/RnPbBe/output/
v11-01b w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01b/RnPbBe/output/
v11-01d w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01d/RnPbBe/output/

--Melissa Sulprizio (talk) 20:22, 30 October 2015 (UTC)

Budget of Pb210

In this table we plot the budgets of Pb²¹⁰ obtained from 1-year benchmark simulations at 4° x 5° resolution done with various GEOS-Chem versions.

Version	Met Field	Year	Tropospheric burden [g]	Tropospheric lifetime against deposition [days]	Sources [g day -1]		Sinks [g day-1]
					From Stratosphere	From Troposphere	Dry Deposition	Wet Deposition			Radioactive decay
								Total	Stratiform	Convective
v8-03-02	GEOS-5	2005	298.318	9.01288	0.129642	32.9831	3.21013	29.8775	21.3283	8.54923	0.0266710
v9-01-01	GEOS-5	2005	316.253	9.55568	0.129852	32.9831	3.66397	29.4223	19.4090	10.0134	0.0251665
v9-01-02	GEOS-5	2005	317.884	9.60957	0.121441	32.9831	3.49208	29.5857	19.5148	10.0709	0.0268078
v9-01-03e	GEOS-5	2005	314.790	9.51050	0.128670	32.9831	3.48612	29.5991	20.8285	8.77061	0.0265495
v9-02r	GEOS-5	2012/2013	305.699	9.25835	0.419521	32.6109	3.42747	29.5772	20.2059	9.37127	0.0257354
v9-02r	GEOS-FP	2012/2013	247.630	7.71356	0.143133	31.9904	3.15887	28.9538	22.5351	6.41867	0.0208565
v10-01	GEOS-FP	2013	250.912	7.77516	0.0832825	32.2152	3.51910	28.7582	22.0207	6.73749	0.0211769
v11-01b	GEOS-FP	2013	212.655	6.60214	0.228550	31.9528	3.49478	28.6686	22.0420	6.62657	0.0179612
v11-01d	GEOS-FP	2013	210.371	6.54296	0.225956	31.9538	3.41587	28.7451	21.9070	6.83813	0.0177696

NOTES:

• The simulations that utilized GEOS-5 met fields were done for year 2005, with a 4-year spinup. (Computed by Hongyu Liu)
• The benchmark simulations for v9-02r were done for June 2012–May 2013, with a 2-month spinup. This was due to data availability of the GEOS-FP met fields at the time of the simulation. (Completed by Karen Yu)
• The simulations for GEOS-Chem v10-01 and later versions utilized GEOS-FP met fields for the year 2013, with a 4-year spinup. (Completed by the GEOS-Chem Support Team)
• Hongyu Liu and Bo Zhang are investigating the low Pb tropospheric lifetime against deposition observed in v11-01b using GEOS-FP. A quick fix was tested in v11-01d, but subsequently removed because of the high impact on aerosols. For more information, see this discussion on the Wet deposition wiki page.

--Melissa Sulprizio (talk) 15:55, 4 December 2015 (UTC)

Budget of Be7

In this table we plot the budgets of Be⁷ obtained from 1-year benchmark simulations at 4° x 5° resolution done with various GEOS-Chem versions.

Version	Met Field	Year	Tropospheric burden [g]	Tropospheric lifetime against deposition [days]	Sources [g day -1]		Sinks [g day-1]
					From Stratosphere	From Troposphere	Dry Deposition	Wet Deposition			Radioactive decay
								Total	Stratiform	Convective
v8-03-02	GEOS-5	2005	4.31961	33.9930	0.0504585	0.132552	0.00808056	0.118666	0.0846774	0.0339885	0.0562636
v9-01-01	GEOS-5	2005	4.39407	34.8514	0.0504328	0.132552	0.00969345	0.116060	0.0767926	0.0392671	0.0572312
v9-01-02	GEOS-5	2005	4.39653	34.8814	0.0504253	0.132552	0.00936374	0.116350	0.0769681	0.0393817	0.0572633
v9-01-03e	GEOS-5	2005	4.37787	34.6750	0.0504472	0.132552	0.00882144	0.117156	0.0858211	0.0393817	0.0570217
v9-02r	GEOS-5	2012/2013	3.49564	27.5376	0.0674867	0.104750	0.00881422	0.117906	0.0844566	0.0334494	0.0455165
v9-02r	GEOS-FP	2012/2013	3.41039	25.9787	0.0630964	0.112349	0.00782526	0.123206	0.1093560	0.0138500	0.0444134
v10-01	GEOS-FP	2013	3.98942	30.1194	0.0512072	0.132977	0.00794288	0.124298	0.1101450	0.0141529	0.0519433
v11-01b	GEOS-FP	2013	3.33530	23.3408	0.0530463	0.132914	0.00698390	0.135539	0.1228950	0.0126441	0.0434378
v11-01d	GEOS-FP	2013	3.32564	23.2523	0.0530363	0.132914	0.00664940	0.135989	0.122347	0.0136424	0.0433123

NOTES:

• The simulations that utilized GEOS-5 met fields were done for year 2005, with a 4-year spinup. (Computed by Hongyu Liu)
• The benchmark simulations for v9-02r were done for June 2012–May 2013, with a 2-month spinup. This was due to data availability of the GEOS-FP met fields at the time of the simulation. (Completed by Karen Yu)
• The simulations for GEOS-Chem v10-01 and later versions utilized GEOS-FP met fields for the year 2013, with a 4-year spinup. (Completed by the GEOS-Chem Support Team)

--Melissa Sulprizio (talk) 15:55, 4 December 2015 (UTC)

GEOS-5 vs. MERRA

As demonstrated by Liu et al. (2001), the Rn-Pb-Be simulation is a valuable tool for testing aerosol wet scavenging in the model. Here the Rn-Pb-Be simulation is used to benchmark the differences between several configurations for the current implementation of aerosol wet scavenging in v9-01-02.

Helen Amos ran 4 different 1-year Rn-Pb-Be simulations to look at how Pb²¹⁰ wet deposition is affected by GEOS-5 and MERRA meteorology:

Run 1: GEOS-5 std

Simulation with the standard GEOS-Chem v9-01-02 code, using with GEOS-5 met fields

Run 2: MERRA std

Simulation with the standard GEOS-Chem v9-01-02 code, using with MERRA met fields. This simulation is intended to give the user a sense of the differences to expect between using MERRA and GEOS-5 meteorological fields.

Run 3: MERRA met GEOS-5 wet dep

This simulation was run using GEOS-Chem v9-01-02 with MERRA meteorological fields and the GEOS-5 wet deposition algorithms (in wetscav_mod.F and convection_mod.F). Additional fields were archived for MERRA that were not archived for GEOS-5. These additional fields for MERRA were used to update the wet scavenging algorithms (e.g. precipitation production in MAKE_QQ) in v9-01-01. This simulation is intended to discriminate between the effects of (a) meteorological fields and (b) changes made to the wet deposition algorithms for MERRA.

Run 4: GEOS-5 w/ Wang et al. (2011) aerosol washout

This simulation was run using v9-01-02 with GEOS-5 fields and aerosol washout updated according to Wang et al. (2011, ACPD). This simulation is intended as a preview for what to expect when the Wang et al. (2011) updates go into the standard code in v9-01-03.

All simulations were performed using GEOS-Chem v9-01-02 at 4° x 5° resolution for the year 2009.

Comparison plots

Helen Amos also prepared the following comparison plots from these simulations. All results shown are for GEOS-Chem v9-01-02 at 4° x 5° resolution for the year 2009. Monthly averages for January and July plotted separately.

Comparison
GEOS-5 standard simulation (Run 1) vs. MERRA standard simulation (Run 2)	January	July
GEOS-5 standard simulation (Run 1) vs. MERRA simulation w/ GEOS-5 wetdep algorithms (Run 3)	January	July
GEOS-5 standard simulation (Run 1) vs. GEOS-5 simulation w/ Wang et al (2011) aerosol washout (Run 4)	January	July

--Bob Y. 13:37, 29 November 2011 (EST)

Comparison budgets

Helen Amos also prepared the budgets from each of her 4 simulations. These are compared to the original Rn-Pb-Be simulation as described in Liu et al. (2001).

Version	Tropospheric burden [g]	Tropospheric lifetime against deposition [days]	Sources [g day -1]	Sinks [g day-1]
			Strat + Trop	Dry Deposition	Wet Deposition		Radioactive decay
					Stratiform	Convective
Liu et al. (2001)	299	9	34	3.8	21	9.6	0.03
Run 1 v9-01-02 w/ GEOS-5 std	324.42	9.80	33.11	3.37	18.57	11.14	0.03
Run 2 v9-01-02 w/ MERRA std	299.74	9.05	33.13	3.37	19.22	10.54	0.03
Run 3 v9-01-02 w/ MERRA met + GEOS-5 wetdep	334.35	9.93	33.68	3.37	18.93	11.37	0.00
Run 4 v9-01-02 w/ GEOS-5 met + Wang washout**	339.11	10.26	33.11	3.68	17.17	12.21	0.03

--Bob Y. 13:57, 29 November 2011 (EST)

--Helen Amos 17:56, 12 September 2012 (EST), the labels for "convective" and "stratiform" were switched. Error corrected now. Thanks to Patrick Kim for pointing it out!

**Note: In Run 4, a condensed water content value of 1.5d-6 cm³ H20/cm³ air was used in the calculation of F' in wetscav_mod.F. Qiaoqiao Wang updated this value to 1.0d-6 cm³ H20/cm³ as described in Wang et al. [2011]. The use of 1.0d-6 increases the fraction of precipitating area, resulting in a slightly shorter lifetime of Pb210, as seen in the budget of Pb210 from the 1-year Rn-Pb-Be benchmark simulation for v9-01-03e.

--Melissa Sulprizio (talk) 15:55, 4 December 2015 (UTC)

References

1. Liu, H., D. Jacob, I. Bey, and R.M. Yantosca, Constraints from 210Pb and 7Be on wet deposition and transport in a global three-dimensional chemical tracer model driven by assimilated meteorological fields, J. Geophys. Res, 106, D11, 12,109-12,128, 2001.
2. Jacob et al., Evaluation and intercomparison of global atmospheric transport models using Rn-222 and other short-lived tracers, J. Geophys. Res, 102, 5953-5970, 1997.
3. Koch, D. J. Geophys. Res, 101, D13, 18651, 1996.
4. Lal, D., and B. Peters, Cosmic ray produced radioactivity on the Earth. Handbuch der Physik, 46/2, 551-612, edited by K. Sitte, Springer-Verlag, New York, 1967.

Previous issues that are now resolved

Incorrect Rn values caused by bug in convection_mod.f

The bug in convection_mod.f described here can cause incorrect values of Rn in GEOS-Chem v8-03-01 and prior versions. This was fixed in GEOS-Chem v8-03-02.

--Bob Y. 16:17, 19 May 2011 (EDT)

Bug for ND44 diagnostic in diag3.f

NOTE: This bug was issued as a post-release patch ("v9-01-01-Patch-diags") in GEOS-Chem v9-01-01 and was approved on 07 Jun 2011.

In the ND44 diagnostic section of diag3.f, the following lines are present twice (once for drydep fluxes and again for drydep velocities). This is a special-case for some tracers in the Caltech isoprene scheme:

              ! Special case for tracers with several dry dep. tracers
              ! E.g. ISOPN: ISOPND and ISOPNB.
              ! We handle both tracers at the same time so we need to 
              ! skip the second tracer. (ccc, 2/3/10)
              !IF ( MMB /= NN ) CYCLE
              IF ( MMB /= NN                .OR.
    &              DEPNAME( N ) == 'ISOPNB' .OR.
    &              DEPNAME( N ) == 'MVKN'       ) CYCLE

However, these lines will cause the drydep fluxes and velocities for Be7 to be skipped. The fix is to bracket these lines with an IF statement so that they will only execute for a full-chemistry simulation:

           IF ( ITS_A_FULLCHEM_SIM() ) THEN
              ! Special case for tracers with several dry dep. tracers
              ! E.g. ISOPN: ISOPND and ISOPNB.
              ! We handle both tracers at the same time so we need to 
              ! skip the second tracer. (ccc, 2/3/10)
              !IF ( MMB /= NN ) CYCLE
              IF ( MMB /= NN                .OR.
    &              DEPNAME( N ) == 'ISOPNB' .OR.
    &              DEPNAME( N ) == 'MVKN'       ) CYCLE
           ENDIF

--Bob Y. 11:57, 7 July 2011 (EDT)

Out-of-bounds errors in ND01, ND02 diagnostics

This issue was fixed in GEOS-Chem v9-01-02, just prior to its release.

In RnPbBe_mod.F, the ND01 (Source of Rn, Pb, Be) and ND02 (Decay of Rn, Pb, Be) diagnostics had array-out-of-bounds errors if you requested less than 47 levels.

For example, if you specified these settings in your input.geos file (assuming a GEOS-5 or MERRA simulation w/ 47 levels):

ND01: Rn/Pb/Be source   : 47   all
ND02: Rn/Pb/Be decay    : 47   all

then your run would work just fine. However, if you tried this:

ND01: Rn/Pb/Be source   :  1   all
ND02: Rn/Pb/Be decay    :  1   all

then your run would crash. In some instances, the error masked itself as an I/O error (i.e. "file not found"). This is because an out-of-bounds was probably corrupting the variables that were used to check if all of the data had been read from a particular met field file.

To prevent this from happening, we now test whether the L index is smaller or equal to LD01 (the vertical extent of the AD01 array) or LD02 (the vertical extent of the AD02 array). We have now modified all of the IF statements where the ND01 or ND02 diagnostics are invoked.

For example, we took the existing block of code:

     ! ND01 diag: 7Be emission [kg/s]
     IF ( ND01 > 0 ) THEN
        AD01(I,J,L,3) = AD01(I,J,L,3) + ( ADD_Be / DTSRCE )
     ENDIF

and add an additional test on L:

     ! ND01 diag: 7Be emission [kg/s]
     IF ( ND01 > 0 .and. L <= LD01 ) THEN
        AD01(I,J,L,3) = AD01(I,J,L,3) + ( ADD_Be / DTSRCE )
     ENDIF

etc.

We will add this fix into GEOS-Chem v9-01-02, since it does not affect the full-chemistry simulation.

--Bob Y. 11:08, 28 November 2011 (EST)

Missing drydep diagnostics caused by tracer name error

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

Please use the following tracer names in input.geos when setting up a Rn-Pb-Be simulation:

%%% TRACER MENU %%%     : 
Type of simulation      : 1
Number of Tracers       : 3                      
Tracer Entries -------> : TR#   Name  g/mole   Tracer Members; () = emitted 
Tracer #1               :   1   Rn     222.0  
Tracer #2               :   2   Pb     210.0
Tracer #3               :   3   Be7      7.0

If you use alternate spellings for the Rn and Pb tracers, such as:

Tracer #1               :   1   Rn222  222.0  
Tracer #2               :   2   Pb210  210.0

Then this may cause the dry deposition fluxes and frequencies for Pb²¹⁰ not to be printed out.

A fix is forthcoming in GEOS-Chem v9-01-03.

--Bob Y. 11:57, 7 July 2011 (EDT)

Outstanding issues

Typo in HEMCO extension module hcox_gc_RnPbBe_mod.F90

This issue will be fixed in v11-01f.

Mat Evans wrote:

We’ve just installed fort 16.0.1 (upgrading from 13.0.1).

A bug come up in the compilation of the code for HEMCO/Extensions/hcox_gc_RnPbBe_mod.F where there is essentially a data statement so that 54_hp wouldn’t compile as it was an integer but 54.0_hp would.

In module HEMCO/Extensions/hcox_gc_RnPbBe_mod.F90, we have replaced the text in RED:

   BESOU(:,22) = (/    25.5_hp,     26.5_hp,     32.0_hp,    40.5_hp,    &
                         54_hp,     67.5_hp,     69.5_hp,    69.5_hp,    &
                       69.5_hp,     69.5_hp  /)

with the text in RED:

   BESOU(:,22) = (/    25.5_hp,     26.5_hp,     32.0_hp,    40.5_hp,    &
                       54.0_hp,     67.5_hp,     69.5_hp,    69.5_hp,    &
                       69.5_hp,     69.5_hp  /)

--Bob Yantosca (talk) 16:53, 8 January 2016 (UTC)