Difference between revisions of "TransportTracers simulation"
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== Dry deposition == | == Dry deposition == | ||
| − | The following updates were made to | + | The following dry deposition updates were recently made to the GEOS-Chem Rn-Pb-Be simulation: |
=== GEOS-Chem v10-01 === | === GEOS-Chem v10-01 === | ||
Revision as of 20:36, 15 June 2015
This page contains information about the Radon-Lead-Beryllium simulation in GEOS-Chem.
Contents
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:
- Rn222, which is emitted naturally from soils
- Pb210, which is the primary decay product of Rn222
- 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]):
| ||||||||||||
| Pb210 | Radioactive decay from Rn222 according to the exponential law:
Where ΔT is the emission timestep in seconds. | ||||||||||||
| Be7 | The source of Be7 is taken from the following reference:
with the following modifications (cf. Liu et al [2001]):
|
--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:
|
no | no |
| Pb210 | Decays according to the exponential law:
|
yes | yes |
| Be7 | Decays according to the exponential law:
|
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:
- Routine DRYFLXRnPbBe—which is where dry deposition losses had been applied to the Pb210 and Be7 in prior GEOS-Chem versions—has now been removed from module GeosCore/drydep_mod.F
- The ND44 diagnostic (archival of Pb210 and Be7 dry deposition fluxes) is now handled by routine DO_TEND in module GeosCore/mixing_mod.F90. This was formerly done in routine DRYFLXRnPbBe.
- 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.
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
--Melissa Sulprizio (talk) 18:28, 15 June 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.
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)
| Quantity | v8-03-02 w/ GEOS-5 |
v9-01-01 w/ GEOS-5 |
v9-01-02 w/ GEOS-5 |
v9-01-03e w/ GEOS-5 |
v9-02r w/ GEOS-5 |
v9-02r w/ GEOS-FP |
v10-01 w/ GEOS-FP |
|---|---|---|---|---|---|---|---|
| Burden (g) | 298.318 | 316.253 | 317.884 | 314.790 | 305.699 | 247.630 | 250.912 |
| Residence time (days) | 9.01288 | 9.55568 | 9.60957 | 9.51050 | 9.25835 | 7.71356 | 7.77516 |
| Sources (g day-1) | |||||||
from Stratosphere
|
0.129642 | 0.129852 | 0.121441 | 0.128670 | 0.419521 | 0.143133 | 0.0832825 |
within Troposphere
|
32.9831 | 32.9831 | 32.9831 | 32.9831 | 32.6109 | 31.9904 | 32.2152 |
| Sinks (g day-1) | |||||||
Dry Deposition
|
3.21013 | 3.66397 | 3.49208 | 3.48612 | 3.42747 | 3.15887 | 3.51910 |
Wet Deposition
|
29.8775 | 29.4223 | 29.5857 | 29.5991 | 29.5772 | 28.9538 | 28.7582 |
Stratiform
|
21.3283 | 19.4090 | 19.5148 | 20.8285 | 20.2059 | 22.5351 | 22.0207 |
Convective
|
8.54923 | 10.0134 | 10.0709 | 8.77061 | 9.37127 | 6.41867 | 6.73749 |
Radioactive decay
|
0.0266710 | 0.0251665 | 0.0268078 | 0.0265495 | 0.0257354 | 0.0208565 | 0.0211769 |
--Melissa Sulprizio (talk) 18:28, 15 June 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.
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)
| Quantity | v8-03-02 w/ GEOS-5 |
v9-01-01 w/ GEOS-5 |
v9-01-02 w/ GEOS-5 |
v9-01-03e w/ GEOS-5 |
v9-02r w/ GEOS-5 |
v9-02r w/ GEOS-FP |
v10-01 w/ GEOS-FP |
|---|---|---|---|---|---|---|---|
| Burden (g) | 4.31961 | 4.39407 | 4.39653 | 4.37787 | 3.49564 | 3.41039 | 3.98942 |
| Residence time (days) | 33.9930 | 34.8514 | 34.8814 | 34.6750 | 27.5376 | 25.9787 | 30.1194 |
| Sources (g day-1) | |||||||
from Stratosphere
|
0.0504585 | 0.0504328 | 0.0504253 | 0.0504472 | 0.0674867 | 0.0630964 | 0.0512072 |
within Troposphere
|
0.132552 | 0.132552 | 0.132552 | 0.132552 | 0.104750 | 0.112349 | 0.132977 |
| Sinks (g day-1) | |||||||
Dry Deposition
|
0.00808056 | 0.00969345 | 0.00936374 | 0.00882144 | 0.00881422 | 0.00782526 | 0.00794288 |
Wet Deposition
|
0.118666 | 0.116060 | 0.116350 | 0.117156 | 0.117906 | 0.123206 | 0.124298 |
Stratiform
|
0.0846774 | 0.0767926 | 0.0769681 | 0.0858211 | 0.0844566 | 0.1093560 | 0.1101450 |
Convective
|
0.0339885 | 0.0392671 | 0.0393817 | 0.0313346 | 0.0334494 | 0.0138500 | 0.0141529 |
Radioactive decay
|
0.0562636 | 0.0572312 | 0.0572633 | 0.0570217 | 0.0455165 | 0.0444134 | 0.0519433 |
--Melissa Sulprizio (talk) 18:28, 15 June 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).
| Quantity | Liu et al (2001) |
(Run 1) v9-01-02 GEOS-5 std |
(Run 2) v9-01-02 MERRA std |
(Run 3) v9-01-02 MERRA met GEOS-5 wetdep |
(Run 4) v9-01-02 GEOS-5 met w/ Wang aerosol washout** |
|---|---|---|---|---|---|
| Burden (g) | 299 | 324.42 | 299.74 | 334.35 | 339.11 |
| Residence time (days) | 9 | 9.80 | 9.05 | 9.93 | 10.26 |
| Sources (g day-1) | |||||
Strat + Trop
|
34 | 33.11 | 33.13 | 33.68 | 33.11 |
| Sinks (g day-1) | |||||
Dry Deposition
|
3.8 | 3.37 | 3.37 | 3.37 | 3.68 |
Wet Deposition
|
|||||
Stratiform
|
21 | 18.57 | 19.22 | 18.93 | 17.17 |
Convective
|
9.6 | 11.14 | 10.54 | 11.37 | 12.21 |
Radioactive decay
|
0.03 | 0.03 | 0.03 | 0.00 | 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 Payer 17:34, 24 January 2012 (EST)
References
- 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.
- 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.
- Koch, D. J. Geophys. Res, 101, D13, 18651, 1996.
- 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)
