TransportTracers simulation: Difference between revisions

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--[[User:Bmy|Bob Y.]] 11:57, 7 July 2011 (EDT)
--[[User:Bmy|Bob Y.]] 11:57, 7 July 2011 (EDT)
=== Out-of-bounds errors in ND01, ND02 diagnostics ===
[[Image:Obsolete.jpg]]
<span style="color:red">'''''NOTE: In [[GEOS-Chem v10-01]] and higher versions, diagnostics for emissions of Rn and Be are archived by [[HEMCO]].'''''</span>
<span style="color:green">'''''This issue was fixed in [[GEOS-Chem v9-01-02]], just prior to its release.'''''</span>
In <tt>RnPbBe_mod.F</tt>, the ND01 (Source of Rn, Pb, Be) and ND02 (Decay of Rn, Pb, Be) diagnostics had [[Common GEOS-Chem error messages#Array-out-of-bounds|array-out-of-bounds errors]] if you requested less than 47 levels. 
For example, if you specified these settings in your <tt>input.geos</tt> 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.
--[[User:Bmy|Bob Y.]] 11:08, 28 November 2011 (EST)

Revision as of 20:43, 15 May 2018

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. PASV, an optional passive species (in GEOS-Chem v11-01 and newer versions).

This simulation is most frequently used to validate the convection, advection, and wet scavenging 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.

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]):

  1. 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
  2. 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
PASV Passive species (optional).

Passive species definition

  • You can specify the species name, molecular weight and an emissions flux in the PASSIVE SPECIES MENU section of input.geos.
  • The "out-of-the-box" settings in input.geos for the Rn-Pb-Be-PASV simulation are:
    • Passive species name: PASV
    • Passive species molecular weight: -1
    • Default background concentration: 1.0e-7 v/v

Passive species emissions flux

  • You can specify an emissions flux for the passive species in the HEMCO configuration file (HEMCO_Config.rc), as described on the Passive species section of our HEMCO examples wiki page.
  • The "out-of-the-box" settings in HEMCO_Config.rc for the Rn-Pb-Be-PASV simulation are:
    • Passive species emissions flux: none

--Bob Yantosca (talk) 15:07, 18 May 2017 (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)

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
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
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
v11-01f GEOS-FP 2013 204.931 6.37746 0.225323 31.9356 3.32210 28.8216 22.2060 6.61553 0.0172499
v11-01f MERRA-2 2013 199.426 6.20202 0.237400 31.9437 3.26365 28.9007 21.7525 7.14814 0.0167875
v11-01h GEOS-FP 2013 205.551 6.37603 0.200768 32.0656 3.32588 28.9232 22.2968 6.62642 0.0173020
v11-01i GEOS-FP 2013 229.335 7.10581 0.219894 32.0656 3.90206 28.3642 19.9163 8.44786 0.0192984
v11-02b GEOS-FP 2013 229.061 7.09725 0.219669 32.0661 3.93661 28.3299 19.8931 8.43679 0.0192754
v11-02e GEOS-FP 2013 229.338 7.10583 0.219864 32.0661 3.90212 28.3646 19.9166 8.44793 0.0192987
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 (72L) 2016 217.941 6.71192 0.224 32.2206 3.94971 28.4770 20.0147 8.46232 0.00183407

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. 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
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
v11-01f GEOS-FP 2013 3.27720 22.8066 0.0531204 0.132842 0.00628201 0.137021 0.124239 0.0127822 0.0426591
v11-01f MERRA-2 2013 3.12435 21.2728 0.0538848 0.133202 0.00650753 0.139910 0.124784 0.0151255 0.0406699
v11-01h GEOS-FP 2013 3.27337 22.7988 0.0531059 0.132685 0.00626941 0.136914 0.124153 0.0127610 0.0426082
v11-01i GEOS-FP 2013 3.51044 24.9815 0.0531920 0.132685 0.0102795 0.129907 0.103831 0.0260760 0.0456914
v11-02b GEOS-FP 2013 3.51002 24.9773 0.0531920 0.132688 0.0103364 0.129856 0.103796 0.0260605 0.0456861
v11-02e GEOS-FP 2013 3.51047 24.9816 0.0531919 0.132687 0.0102796 0.129907 0.103831 0.0260759 0.0456918
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 (72L) 2016 3.56036 24.6000 0.0543652 0.136303 0.00955045 0.134776 0.108970 0.0258063 0.0463413

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. The results reported here are for simulations using the non-local PBL mixing (VDIFF) scheme. (Completed by the GEOS-Chem Support Team)

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)

Radon flux diagnostic

This update will be added in GEOS-Chem v11-02

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, 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

Typo in HEMCO extension module hcox_gc_RnPbBe_mod.F90

This fix was included in v11-01f (approved 16 Apr 2016).

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. The value 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 GREEN: 

   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) 15:34, 30 March 2016 (UTC)

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)

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)

Outstanding issues

None at this time

Obsolete information

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

Bug for ND44 diagnostic in diag3.f

NOTE: This code was removed during the implementation of the species database in GEOS-Chem v11-01.

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

Obsolete.jpg

NOTE: In GEOS-Chem v10-01 and higher versions, diagnostics for emissions of Rn and Be are archived by HEMCO.

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)

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