TransportTracers simulation

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1. Simulations overview
2. Mechanisms for full-chemistry simulations (e.g. Standard, Tropchem, etc.)
3. Aerosol-only simulation
4. CH4 simulation
5. CO2 simulation
6. Hg simulation
7. POPs simulation
8. Tagged CO simulation
9. Tagged O3 simulation
10. TransportTracers simulation

This page contains information about the Radon-Lead-Beryllium (and optional passive species) 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
4. Be¹⁰, which is produced by cosmic rays in the stratosphere and upper atmosphere (introduced in GEOS-Chem 12.2.0)

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

Starting in GEOS-Chem 12.2.0, the Rn-Pb-Be simulation has been expanded to include several passive species in a new "Transport Tracer simulation." Please see this wiki post for more information.

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.

Sources

Species	Chemical source
Rn222	The default source of Rn222 follows 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 In GEOS-Chem 13.4.0 and later versions, users will have the option of replacing the default Rn222 emissions (described above) with emissions from Bo Zhang et al [2021] (DOI: 10.5194/acp-21-1861-2021).
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 from 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
Be10	Be10 has an identical source distribution as Be7 following Koch and Rind (1998).

--Melissa Sulprizio (talk) 13:56, 4 January 2019 (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	Half-life of 3.83 days (Liu at al., 2001). Decays into Pb210 according to the exponential law: EXP( -ΔT * 2.097d-6 )	no	no
Pb210	Half-life of 22.3 years (Liu et al., 2001). Decays according to the exponential law: EXP( -ΔT * 9.725d-10 )	yes	yes
Be7	Half-life of 53.3 days (Liu et al., 2001). Decays according to the exponential law: EXP( -ΔT * 1.506d-7 )	yes	yes
Be10	Half-life of 5.84e8 days (Koch and Rind, 1998). Decays according to the exponential law: EXP( -ΔT * 1.506d-7 )	yes	yes

--Melissa Sulprizio (talk) 13:56, 4 January 2019 (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)

Vertical Grid

This update was included in v11-02e (approved 24 Mar 2018).

Starting in GEOS-Chem v11-02e the default vertical grid used in Rn-Pb-Be simulations is the native 72-level grid for GEOS-FP and MERRA-2.

Lizzie Lundgren wrote:

The RnPbBe uses 47 levels by default (NO_REDUCED=n) for GEOS-Chem Classic and this is what we benchmark. GCHP, however, only uses the full 72 level grid. I recall that using either option gives the same result. I therefore wonder if we could change the GEOS-Chem Classic default to be 72 levels, consistent with GCHP. I do not think this would be significantly more expensive computationally.

--Melissa Sulprizio (talk) 18:08, 16 March 2018 (UTC)

Validation

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

1-year benchmark simulations

Benchmark overview

1-year Rn-Pb-Be benchmark simulations are completed at the request of the Transport Working Group or whenever an update is introduced into the code that will impact transport and/or wet deposition. Each of these benchmarks involve a 4-year spinup period, followed by the 1-year run used for evaluation.

Benchmark plots

Version	Link
12.8.0 w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/GC_12/12.8.0/
12.2.0 w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/GC_12/12.2.0/TransportTracers/output/
v11-02e w/ GEOS-FP (2016 met)	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-02/v11-02e/RnPbBePasv-Run2/NLPBL/output/
v11-02e w/ GEOS-FP (72 levels)	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-02/v11-02e/RnPbBePasv-Run1/NLPBL/output/
v11-02e w/ GEOS-FP (2013 met)	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-02/v11-02e/RnPbBePasv-Run0/NLPBL/output/
v11-02b w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-02/v11-02b/RnPbBePasv/RnPbBePasv_VDIFF/output/
v11-01i w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01i/RnPbBePasv/RnPbBePasv_VDIFF/output/
v11-01h w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01h/RnPbBePasv/RnPbBePasv_VDIFF/output/
v11-01f w/ MERRA-2	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/MERRA2/RnPbBe/RnPbBePasv_VDIFF/output/
v11-01f w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/GEOSFP/RnPbBe/RnPbBePasv_VDIFF/output/
v11-01d w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01d/RnPbBe/RnPbBePasv_VDIFF/output/
v11-01b w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01b/RnPbBe/output/
v10-01 w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01-public-release/RnPbBe/output/
v9-02r w/ GEOS-FP	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-02/v9-02r/geosfp/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/
v9-01-03e w/ GEOS-5	http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/RnPbBe/output/pdf/
v9-01-02 w/ GEOS-5	http://wiki.seas.harvard.edu/geos-chem/index.php/Rn-Pb-Be_simulation#Comparison_plots

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
12.8.0 (with Luo2019 wetdep)	GEOS-FP (72L)	2016	105.1827	3.2461	0.2690	32.1142	2.3068	30.0303	25.4236	4.6067	0.0088608
12.8.0	GEOS-FP (72L)	2016	211.6465	6.5363	0.2690	32.1142	3.9521	28.4142	19.9437	8.4705	0.0178018
12.2.0	GEOS-FP (72L)	2016	218.330	6.71344	0.236801	32.2602	3.95678	28.5218	20.0439	8.47787	0.0183735
v11-02e	GEOS-FP (72L)	2016	217.941	6.71192	0.224000	32.2206	3.94971	28.4770	20.0147	8.46232	0.0183407
v11-02e	GEOS-FP (72L)	2013	229.338	7.10583	0.219856	32.0661	3.90212	28.3646	19.9166	8.44793	0.0192987
v11-02e	GEOS-FP	2013	229.338	7.10583	0.219864	32.0661	3.90212	28.3646	19.9166	8.44793	0.0192987
v11-02b	GEOS-FP	2013	229.061	7.09725	0.219669	32.0661	3.93661	28.3299	19.8931	8.43679	0.0192754
v11-01i	GEOS-FP	2013	229.335	7.10581	0.219894	32.0656	3.90206	28.3642	19.9163	8.44786	0.0192984
v11-01h	GEOS-FP	2013	205.551	6.37603	0.200768	32.0656	3.32588	28.9232	22.2968	6.62642	0.0173020
v11-01f	MERRA-2	2013	199.426	6.20202	0.237400	31.9437	3.26365	28.9007	21.7525	7.14814	0.0167875
v11-01f	GEOS-FP	2013	204.931	6.37746	0.225323	31.9356	3.32210	28.8216	22.2060	6.61553	0.0172499
v11-01d	GEOS-FP	2013	210.371	6.54296	0.225956	31.9538	3.41587	28.7451	21.9070	6.83813	0.0177696
v11-01b	GEOS-FP	2013	212.655	6.60214	0.228550	31.9528	3.49478	28.6686	22.0420	6.62657	0.0179612
v10-01	GEOS-FP	2013	250.912	7.77516	0.0832825	32.2152	3.51910	28.7582	22.0207	6.73749	0.0211769
v9-02r	GEOS-FP	2012/2013	247.630	7.71356	0.143133	31.9904	3.15887	28.9538	22.5351	6.41867	0.0208565
v9-02r	GEOS-5	2012/2013	305.699	9.25835	0.419521	32.6109	3.42747	29.5772	20.2059	9.37127	0.0257354
v9-01-03e	GEOS-5	2005	314.790	9.51050	0.128670	32.9831	3.48612	29.5991	20.8285	8.77061	0.0265495
v9-01-02	GEOS-5	2005	317.884	9.60957	0.121441	32.9831	3.49208	29.5857	19.5148	10.0709	0.0268078
v9-01-01	GEOS-5	2005	316.253	9.55568	0.129852	32.9831	3.66397	29.4223	19.4090	10.0134	0.0251665
v8-03-02	GEOS-5	2005	298.318	9.01288	0.129642	32.9831	3.21013	29.8775	21.3283	8.54923	0.0266710

NOTES:

• Bolded text denotes change in meteorology product and/or meteorology year.
• 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. The results reported here are for simulations using the non-local PBL mixing (VDIFF) scheme. (Completed by the GEOS-Chem Support Team)
• The simulations for GEOS-Chem 12.2.0 and later versions utilized GEOS-FP met fields for the year 2016, with a 10-year spinup. The results reported here are for simulations using the non-local PBL mixing (VDIFF) scheme. (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.

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
12.8.0 (with Luo2019 wetdep)	GEOS-FP (72L)	2016	1.1882	9.5228	0.2882	0.1149	0.0052	0.1188	0.1029	0.0159	0.0154770
12.8.0	GEOS-FP (72L)	2016	2.8927	20.5842	0.2882	0.1149	0.0095	0.1305	0.1047	0.0258	0.0376572
12.2.0	GEOS-FP (72L)	2016	3.55540	24.5959	0.0541444	0.136303	0.00952537	0.134645	0.108871	0.0257736	0.0462768
v11-02e	GEOS-FP (72L)	2016	3.56036	24.6000	0.0543652	0.136303	0.00955045	0.134776	0.108970	0.0258063	0.0463413
v11-02e	GEOS-FP (72L)	2013	3.50286	24.9516	0.0529614	0.132687	0.0102709	0.129784	0.103733	0.0260514	0.0455928
v11-02e	GEOS-FP	2013	3.51047	24.9816	0.0531919	0.132687	0.0102796	0.129907	0.103831	0.0260759	0.0456918
v11-02b	GEOS-FP	2013	3.51002	24.9773	0.0531920	0.132688	0.0103364	0.129856	0.103796	0.0260605	0.0456861
v11-01i	GEOS-FP	2013	3.51044	24.9815	0.0531920	0.132685	0.0102795	0.129907	0.103831	0.0260760	0.0456914
v11-01h	GEOS-FP	2013	3.27337	22.7988	0.0531059	0.132685	0.00626941	0.136914	0.124153	0.0127610	0.0426082
v11-01f	MERRA-2	2013	3.12435	21.2728	0.0538848	0.133202	0.00650753	0.139910	0.124784	0.0151255	0.0406699
v11-01f	GEOS-FP	2013	3.27720	22.8066	0.0531204	0.132842	0.00628201	0.137021	0.124239	0.0127822	0.0426591
v11-01d	GEOS-FP	2013	3.32564	23.2523	0.0530363	0.132914	0.00664940	0.135989	0.122347	0.0136424	0.0433123
v11-01b	GEOS-FP	2013	3.33530	23.3408	0.0530463	0.132914	0.00698390	0.135539	0.1228950	0.0126441	0.0434378
v10-01	GEOS-FP	2013	3.98942	30.1194	0.0512072	0.132977	0.00794288	0.124298	0.1101450	0.0141529	0.0519433
v9-02r	GEOS-FP	2012/2013	3.41039	25.9787	0.0630964	0.112349	0.00782526	0.123206	0.1093560	0.0138500	0.0444134
v9-02r	GEOS-5	2012/2013	3.49564	27.5376	0.0674867	0.104750	0.00881422	0.117906	0.0844566	0.0334494	0.0455165
v9-01-03e	GEOS-5	2005	4.37787	34.6750	0.0504472	0.132552	0.00882144	0.117156	0.0858211	0.0393817	0.0570217
v9-01-02	GEOS-5	2005	4.39653	34.8814	0.0504253	0.132552	0.00936374	0.116350	0.0769681	0.0393817	0.0572633
v9-01-01	GEOS-5	2005	4.39407	34.8514	0.0504328	0.132552	0.00969345	0.116060	0.0767926	0.0392671	0.0572312
v8-03-02	GEOS-5	2005	4.31961	33.9930	0.0504585	0.132552	0.00808056	0.118666	0.0846774	0.0339885	0.0562636

NOTES:

• Bolded text denotes change in meteorology product and/or meteorology year.
• 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. The results reported here are for simulations using the non-local PBL mixing (VDIFF) scheme. (Completed by the GEOS-Chem Support Team)
• The simulations for GEOS-Chem 12.2.0 and later versions utilized GEOS-FP met fields for the year 2016, with a 10-year spinup. The results reported here are for simulations using the non-local PBL mixing (VDIFF) scheme. (Completed by the GEOS-Chem Support Team)

Radon flux diagnostic

This update will be added in GEOS-Chem v11-03.

Daniel Jacob wrote:

I suggest adding to the Rn-Pb-Be benchmark simulation a Rn flux diagnostic for a box across the coastal eastern US made up of 2x2 gridboxes in the horizontal and extending up to 3 levels in the vertical. This would allow testing of the horizontal fluxes as well as the vertical fluxes from advection, convection, and PBL mixing. Benchmark success would be measured by mass balance in that box and comparison to previous version. The first order of business will be to test whether we get a good Rn mass balance to test that the flux diagnostics (ND24, ND25, ND26) works.

--Melissa Sulprizio (talk) 21:39, 23 November 2016 (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, 12109-12128, 2001.
2. Jacob et al., Evaluation and intercomparison of global atmospheric transport models using ²²²Rn and other short-lived tracers, J. Geophys. Res, 102, 5953-5970, 1997.
3. Koch, D.M., D.J. Jacob, and W.C. Graustein, Vertical transport of tropospheric aerosols as indicated by ⁷Be and ²¹⁰Pb in a chemical tracer model, J. Geophys. Res, 101, D13, 18651-18666, 1996.
4. Koch, D., and D. Rind, Beryllium 10/beryllium 7 as a tracer of stratospheric transport, J. Geophys. Res., 103, D4, 3907-3917, 1998.
5. 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.

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