Difference between revisions of "Chemistry Working Group"

                    IF ( N == 8 ) THEN
                       TMP1 = State_Chm%Tracers(IX,IY,IZ,IDTSO4) +
    &                         State_Chm%Tracers(IX,IY,IZ,IDTNIT)
                       TMP2 = State_Chm%tracers(IX,IY,IZ,IDTNIT)
                       IF ( TMP1 .GT. 0.0 ) THEN
                          XSTKCF = XSTKCF * ( 1.0e+0_fp - 0.9e+0_fp
    &                            *TMP2/TMP1 )
                       ENDIF
                    ENDIF

Here NIT is added to SO4 but NIT is in different units than SO4. This unit difference can be traced to the definition of IDTRMB, which is only nonzero for species that are in the SMVGEAR mechanism. Since NIT is not a SMVGEAR species, IDTRMB = 0 for NIT and it is therefore skipped in the unit conversion from kg --> molec/cm3 in partition.F.

This issue was discovered during the implementation of FlexChem. In GEOS-Chem v11-01g and later versions, units of NIT are properly accounted for in routine HETN2O5 (found in gckpp_HetRates.F90).

--Melissa Sulprizio (talk) 20:25, 12 September 2016 (UTC)
--Bob Yantosca (talk) 20:27, 31 January 2017 (UTC)

rate of HNO4

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The globchem.dat file is now replaced by the KPP master equation file.

Ellie Browne found a typo in the globchem.dat (GEOS-Chem v8-02-01 and beyond)

A   73 9.52E-05  3.2E+00 -10900 1 P   0.60     0.     0.         
       1.38E+15  1.4E+00 -10900 0     0.00     0.     0.         
      HNO4          +                         M                                
=1.000HO2           +1.000NO2           +                   +

This should be corrected as:

A   73 9.52E-05  3.4E+00 -10900 1 P   0.60     0.     0.         
       1.38E+15  1.1E+00 -10900 0     0.00     0.     0.         
      HNO4          +                         M                                
=1.000HO2           +1.000NO2           +                   + 

The difference is within 2%.

--J Mao. 19:04, 30 Aug 2010 (EDT)
--Bob Yantosca (talk) 20:29, 31 January 2017 (UTC)

near-IR photolysis of HNO4

This update was added to GEOS-Chem v8-02-04.

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The globchem.dat file is now replaced by the KPP master equation file. Also, FAST-JX has now replaced FAST-J photolysis.

1. Since FastJX already takes this into account with cross section data at 574nm, we do not need to redo this in calcrate.f. We can therefore comment out this entire IF block:

2. We need to change the branch ratio of HNO4 photolysis in ratj.d. Change these lines from:

13 HNO4       PHOTON     OH         NO3                  0.00E+00  0.00     33.3  HO2NO2 
14 HNO4       PHOTON     HO2        NO2                  0.00E+00  0.00     66.7  HO2NO2 

to:

13 HNO4       PHOTON     OH         NO3                  0.00E+00  0.00      5.0  HO2NO2 
14 HNO4       PHOTON     HO2        NO2                  0.00E+00  0.00     95.0  HO2NO2

This is based on Jimenez et al. (Quantum yields of OH, HO2 and NO3 in the UV photolysis of HO2NO2, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2005) shows that HO2 yield should be 0.95 and OH yield should be 0.05 for wavelength above 290nm.

This way all the near-IR photolysis will have most weight on HO2 channel(Stark et al., Overtone dissociation of peroxynitric acid (HO2NO2): Absorption cross sections and photolysis products, JOURNAL OF PHYSICAL CHEMISTRY A, 2008).

This update has now been added to the chemistry mechanism documentation file.

--J Mao. 11:00, 26 Oct 2009 (EDT)
--Bob Y. 16:08, 4 November 2011 (EDT)

yield of isoprene nitrates

This update was added to GEOS-Chem v8-03-02 as a post-release patch, and standardized in GEOS-Chem v9-01-01.

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The globchem.dat file is now replaced by the KPP master equation file.

Fabien Paulot found a problem in current chemistry scheme. In GEOS-Chem v8-02-01 and beyond, isoprene nitrates are produced twice: one through channel A and one through 10% loss in channel B. This makes the loss of NOx larger than it should be (18.7% vs. 10%) and also reduces the yield of MVK/MACR/CH2O by about 13%.

A  453 2.70E-12  0.0E+00    350 1 B   0.00     0.     0.         
       5.00E+00  0.0E+00      0 0     0.00     0.     0.         
      RIO2          +     NO                                              
=0.900NO2           +0.900HO2           +0.340IALD          +0.340MVK     
+0.220MACR          +0.560CH2O          +                   +  
          
A  453 2.70E-12  0.0E+00    350 1 A   0.00     0.     0.         
       5.00E+00  0.0E+00      0 0     0.00     0.     0.         
      RIO2          +     NO                                              
=1.000HNO3          +                   +                   +             

So it should be corrected as (no channel A):

A  453 2.70E-12  0.0E+00    350 0 0   0.00     0.     0.         
      RIO2          +     NO                                              
=0.900NO2           +0.900HO2           +0.340IALD          +0.340MVK     
+0.220MACR          +0.560CH2O          +                   +       

D  453 2.70E-12  0.0E+00    350 1 A   0.00     0.     0.         
       5.00E+00  0.0E+00      0 0     0.00     0.     0.         
      RIO2          +     NO                                              
=1.000HNO3          +                   +                   +  

--J Mao. 18:04, 30 Aug 2010 (EDT)
--Bob Yantosca (talk) 20:31, 31 January 2017 (UTC)

Potential issue with reading restart.cspec file

This update was tested in the 1-month benchmark simulation v9-01-02c and approved on 21 Jul 2011.

The binary-punch format restart.cspec.YYYYMMDDhh file is slated to be replaced by a netCDF-format restart file, starting in GEOS-Chem v11-01 and higher versions. But during a transition period, you can still request binary-punch format output.

Jingqiu Mao discovered a mis-indexing problem when using the restart.cspec.YYYYMMDDhh file. Please see this wiki post for more information.

--Bob Y. 16:02, 4 November 2011 (EDT)
--Bob Yantosca (talk) 20:33, 31 January 2017 (UTC)

GLCO3, GLPAN bug in standard mechanism

This update was tested in the 1-month benchmark simulation v9-01-03a and approved on 08 Dec 2011.

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The globchem.dat file is now replaced by the KPP master equation file.

Fabien Paulot wrote:

I think there is a relatively serious bug in the standard chemistry. GLPAN and GLCO3 are set to inactive but their production and loss reactions are active. As a result they never reach equilibrium and this results in an artificial loss of NOx.

If this is the only cause of the imbalance between sources and sinks of NOx in my simulations, this would account for ~5% of NOy losses. I don't see that problem in a simulation with a different chemistry that among other changes does not feature those reactions. So hopefully that's it.

To fix the error, I made the following modifications in globchem.dat:

1. I set GLPAN and GLCO3 rxns from active to dead. These rxns were causing an artificial loss of NOx.
2. I have physically removed GLCO3, GLP, GLPAN, GPAN, ISNO3, MNO3, O2CH2OH, MVN2 and their associated reactions.
3. I have made GLYX active. I'm not sure why it's not active by default.

and to ratj.d:

1. I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in globchem.dat

--Bob Y. 14:51, 10 November 2011 (EST)
--Melissa Payer 10:49, 15 December 2011 (EST)
--Bob Yantosca (talk) 20:35, 31 January 2017 (UTC)

Bug in routine ARSL1K

This update was tested in the 1-month benchmark simulation v9-01-03m and approved on 06 Jun 2012.

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The ARSL1K routine was replaced by an equivalent function in KPP's rate law library.

A bug in routine ARSL1K became problematic in the implementation of Justin Parrella's tropospheric bromine chemistry mechanism for GEOS-Chem v9-01-03. In the bromine chemistry mechanism, a sticking coefficient of 0.0 is passed to the routine ARSL1K for non-sulfate, non-sea salt aerosol. The IF statement modified in GEOS-Chem v8-02-04 resulted in the reaction rate being set to the default value of 1.0d-3. A 1-month benchmark for July 2005 indicated that the simulated BrO was a little more than twice the expected zonal mean. Modifying the default value from 1.0d-3 to 1.0d-30 resulted in reasonable simulated BrO values.

Mat Evans wrote:

I've re-run two 2 month simulation [using GEOS-Chem v9-01-02]. One with the error handling value of 1e-3 (standard) and one with it being 1e-30. There are 5127 time and space points where the model traps the problem and invokes the 1e-3 or 1e-30 value. There are 30*24*2*37*72*46 (roughly 200 million) time and space points when the error could have occurred so we are looking at a relatively infrequent event.

The simulations show virtually no difference between the two simulations.

mean and stddev ratio of all grid boxes with and without the fix are shown below

    NOx     0.999996  0.000409291
    Ox      1.00000   1.27233e-05
    O3      1.00000   1.52284e-05
    PAN     0.997849  0.0111997
    CO      1.00000   4.21768e-06
    ALK4    0.990514  0.0351941
    ISOP    0.999979  0.0108033
    H2O2    0.992067  0.0264659
    DST1    1.00000   0.00000
    HO2     0.999996  0.00309464
    OH      1.00003   0.00767954

So although there are some differences they are very minor. For completeness we should put this in as a bug fix (make the error value 1d-30 rather than 1d-3). But it is not a major problem.

--Melissa Payer 17:52, 14 May 2012 (EDT)
--Bob Yantosca (talk) 20:35, 31 January 2017 (UTC)

Documentation

• Updated chemical reactions that will be used in GEOS-Chem v8-02-04 and higher.
• Updated chemical reactions now used in GEOS-Chem v8-02-01 through GEOS-Chem v8-02-03.
  • All typos have now been corrected in the present file.
• Format of FAST-J input file jv_spec.dat

--Bob Y. 15:41, 27 October 2009 (EDT)