Difference between revisions of "GEOS-Chem v8-01-03"

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BETA RELEASE December 2008
 
BETA RELEASE December 2008
  
Contains everything in [[GEOS-Chem v8-01-02]] plus the following updates:
+
*Previous version: [[GEOS-Chem v8-01-02]]
 +
*Next version: [[GEOS-Chem v8-01-04]]
  
* [[Previous issues now resolved in v8-01-03#TPCORE replaced with version based on GMI model|Installation of new version of TPCORE (based on GMI model) to fix polar overshoot in stratosphere]]
+
=== What's new in this version ===
* [[Previous issues now resolved in v8-01-03#Output of ND51 does not match output in the ctm.bpch file|Minor bug fix for ND51 diagnostic]]
+
 
* [[Previous issues now resolved in v8-01-03#Bug fixes in diag3.f|Minor bug fixes in diag3.f]]
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Contains everything in [[GEOS-Chem v8-01-02|v8-01-02]] plus the following updates:
* [[Previous_issues_now_resolved_in_v8-01-03#Change_of_location_of_calls_to_diagnostics_in_main.f|Minor diagnostic fixes in main.f]]
+
 
 +
* [[#TPCORE replaced with version based on GMI model|Installation of new version of TPCORE (based on GMI model) to fix polar overshoot in stratosphere]]
 +
* [[#Output of ND51 does not match output in the ctm.bpch file|Minor bug fix for ND51 diagnostic]]
 +
* [[#Bug fixes in diag3.f|Minor bug fixes in diag3.f]]
 +
* [[#Change_of_location_of_calls_to_diagnostics_in_main.f|Minor diagnostic fixes in main.f]]
  
 
== Previous issues now resolved in v8-01-03==
 
== Previous issues now resolved in v8-01-03==
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=== TPCORE replaced with version based on GMI model ===
 
=== TPCORE replaced with version based on GMI model ===
  
==== Overview ====
+
Please see [[Advection scheme TPCORE#TPCORE replaced with version based on GMI model|the discussion on our TPCORE wiki page]] about the implementation of the GMI version of TPCORE into GEOS-Chem.
  
Dylan Jones and Hongyu Liu both independently found thaat the existing TPCORE transport code used to perform the advection for GEOS-4 and GEOS-5 meteorology (<tt>tpcore_fvdas_mod.f90</tt>, by S-J Lin and Kevin Yeh) causes an overshooting in the polar stratopsheric regions.  Claire Carouge has supplied a fix for this issue.
+
Also see [http://acmg.seas.harvard.edu/geos/wiki_docs/advection/tpcore_fvdas.pdf this PDF document] for more information about the new TPCORE version as installed in [[GEOS-Chem versions under development#v8-01-03|GEOS-Chem v8-01-03]].
  
'''''[mailto:hyl@nianet.org Hongyu Liu] wrote:'''''
+
--[[User:Bmy|Bob Y.]] 09:42, 17 February 2010 (EST)
  
:[Here are] the radon plots for all GEOS series as well as the info on GEOS-Chem version and met field version.  This is much less of a problem (or not a problem at all) in GEOS-Chem/GEOS-STRAT and GEOS-Chem/GEOS-3. Actually GEOS-Chem/GEOS-STRAT is very close to GMI/GEOS-STRAT (not shown).  Compare plots below.  All these simulations use same options for tpcore (IORD=3, JORD=3, KORD=7).
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=== Output of ND51 does not match output in the ctm.bpch file ===
  
:*[http://research.nianet.org/~hyl/temp/rnpbbe_geoss_geoschem_zm.Rn.color.1996.yr2.pdf GEOS-Chem v5-05 (GEOS-STRAT)]
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<span style="color:darkorange">'''''NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.'''''</span>
:*[http://research.nianet.org/~hyl/temp/rnpbbe_geos3_geoschem_zm.Rn.color.2001.yr2.pdf  GEOS-Chem v7-04 (GEOS-3)]
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:*[http://research.nianet.org/~hyl/temp/rnpbbe_geos4_geoschem_zm.gmi_rn_emiss_dao_lwi_258K.Rn.color.2004.yr6.pdf GEOS-Chem v7-01-02 (GEOS-4)]
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:*[http://research.nianet.org/~hyl/temp/rnpbbe_geos5_geoschem_zm.258K_no_rainout_conv.geos5_72L.Rn.color.2005.yr2.pdf GEOS-Chem v8-01-01 (GEOS-5)]
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:It seems that GMI does not have this problem. You might want to compare the plots on Pages 7 & 10 [http://gmi.gsfc.nasa.gov/mtgs_rpts/2008_03/HLiu_radionuclides.pdf of this PDF file].
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+
'''''[mailto:dbj@atmosp.physics.toronto.edu Dylan Jones] wrote:'''''
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:Attached are the [http://acmg.seas.harvard.edu/geos/wiki_docs/advection/dave_CO-O3_slides011008.ppt PowerPoint slides].  We added slide 9 which compares the mixed layer depth for GEOS-Chem (with GEOS-5) and GMI (with GEOS-4); we see the same problem in GEOS-Chem with GEOS-5, but we do not see it in GMI.
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:All the GEOS-4 GEOS-Chem runs were with version v7-02-04. The GEOS-5 GEOS-Chem runs were with v8-01-01.
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+
'''''[mailto:ccarouge@seas.harvard.edu Claire Carouge] replied:'''''
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+
:I think I finally got tpcore to work.  [http://acmg.seas.harvard.edu/geos/wiki_docs/advection/plots_pfixer.pdf You have some plots attached for Radon].  So far, I ran 5 months of simulation and each month looks much better: no polar spike and much much lower stratospheric tracer. The concentration of Radon is never null in the stratosphere but I don't think it is in GMI neither, I think the range on the plot was cut off.  So I did the plot with the same cut off. Let me know if you see something strange I haven't seen.
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+
:I don't know for sure what was the problem but I think it was a problem with the definition of the polar cap. In GEOS-Chem, we only averaged values for cells at the poles on 1 band of latitude. In GMI, they use what they call an enlarged polar cap and thus they average values at the poles on 2 bands of latitude.
+
 
+
:The pressure fixer was taken from GMI and thus was written for an enlarged polar cap. The parts of the code that were explicitly labelled for the enlarged polar cap had been removed but not other parts that were not explicitly labelled. So we ended up with a hybrid pressure fixer used with a tpcore with a not enlarged olar cap. I'm guessing this was creating the polar spikes.
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:But, the tpcore in GEOS-Chem and GMI are not easy to compare. I'm not sure there was not a difference in the transport itself and I can't be totally sure the pressure fixer was well introduced in tpcore. I have some doubts about this.
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:So as GMI was an example of a working (and clean!) algorithm with the enlarged polar cap, I decided to introduce the enlarged polar cap in GEOS-Chem. For this:
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:#I slightly modified the pressure-fixer to return to the exact version from GMI
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:#I changed tpcore to the one from GMI as I was sure the pressure fixer was well introduced in (and the algorithm is cleaner).
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'''''[mailto:dbj@atmosp.physics.toronto.edu Dylan Jones] wrote:'''''
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:Claire,
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:Attached are some comparisons of the CO/O3 correlations in the UTLS with the new tpcore.
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:*[http://acmg.seas.harvard.edu/geos/wiki_docs/advection/CO_O3_lat36_76_lon0_25_20060301_gmi_geos4.png CO_O3_lat36_76_lon0_25_20060301_gmi_geos4.png]
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:*[http://acmg.seas.harvard.edu/geos/wiki_docs/advection/CO_O3_lat36_76_lon0_25_alt4_19_200512_gmi_geos.png CO_O3_lat36_76_lon0_25_alt4_19_200512_gmi_geos.png]
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:* [http://acmg.seas.harvard.edu/geos/wiki_docs/advection/CO_O3_lat36_76_lon0_25_20051201_gmi_geos4_tpcore.png CO_O3_lat36_76_lon0_25_20051201_gmi_geos4_tpcore.png]
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:*[http://acmg.seas.harvard.edu/geos/wiki_docs/advection/CO_O3_lat36_76_lon0_25_20060301_gmi_geos4_tpcore.png CO_O3_lat36_76_lon0_25_20060301_gmi_geos4_tpcore.png]
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:The files called <tt>*.gmi_geos.png</tt> are with the old version of tpcore and those called <tt>*.gmi_geos4_tpcore</tt> are with the corrected tpcore. As you can see, there is much less scatter in the  correlations, which suggest less anomalous mixing with the new code.  The scatter is more similar to what we see in GMI. There is still an offset in the stratosphere (for high ozone in the plots), but I think this may be due to linoz rather than to the transport scheme. This is  a huge improvement for GEOS-Chem. Thanks very much for fixing it.
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'''''[mailto:hyl@nianet.org Hongyu Liu] replied:'''''
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:Thanks Claire! Well done. It's clear that the polar overshooting problem is now fixed.
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==== Documentation ====
+
 
+
Please see [http://acmg.seas.harvard.edu/geos/wiki_docs/advection/tpcore_fvdas.pdf this PDF document] for more information about the new TPCORE version as installed in [[GEOS-Chem versions under development#v8-01-03|GEOS-Chem v8-01-03]].
+
 
+
--[[User:Bmy|Bob Y.]] 14:14, 15 December 2008 (EST)
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+
=== Output of ND51 does not match output in the ctm.bpch file ===
+
  
 
'''''[mailto:ccarouge@seas.harvard.edu Claire Carouge] wrote:'''''
 
'''''[mailto:ccarouge@seas.harvard.edu Claire Carouge] wrote:'''''
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=== ND22 (J-value) diagnostic ===
 
=== ND22 (J-value) diagnostic ===
 +
 +
<span style="color:darkorange">'''''NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.'''''</span>
  
 
A problem was discovered in the ND22 diagnostic.  If you typed the following in the diagnostic section of the <tt>input.geos</tt> file:
 
A problem was discovered in the ND22 diagnostic.  If you typed the following in the diagnostic section of the <tt>input.geos</tt> file:
Line 110: Line 66:
  
 
=== ND34 (biofuel emissions) diagnostic ===
 
=== ND34 (biofuel emissions) diagnostic ===
 +
 +
<span style="color:darkorange">'''''NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.'''''</span>
  
 
Prasad Kasibhatla pointed out an inconsistency in the biofuel emissions diagnostics ND29 (slot #3) and ND34.  There was a problem in the writing of ND34 when asking for a subset of tracers only.  The code doesn't write out the array parts corresponding to the tracers asked for.
 
Prasad Kasibhatla pointed out an inconsistency in the biofuel emissions diagnostics ND29 (slot #3) and ND34.  There was a problem in the writing of ND34 when asking for a subset of tracers only.  The code doesn't write out the array parts corresponding to the tracers asked for.
Line 137: Line 95:
  
 
=== DIAG_2PM ===
 
=== DIAG_2PM ===
 +
 +
<span style="color:darkorange">'''''NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.'''''</span>
  
 
We have moved the call to subroutine <tt>DIAG_2PM</tt> to after the call to subroutine <tt>INTERP</tt>.  This will ensure that the correct value of tropopause pressure (TROPP) will be obtained for GEOS-4 met fields.
 
We have moved the call to subroutine <tt>DIAG_2PM</tt> to after the call to subroutine <tt>INTERP</tt>.  This will ensure that the correct value of tropopause pressure (TROPP) will be obtained for GEOS-4 met fields.
Line 146: Line 106:
  
 
=== DIAG1, DIAG41, DIAG42 ===
 
=== DIAG1, DIAG41, DIAG42 ===
 +
 +
<span style="color:darkorange">'''''NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.'''''</span>
  
 
In GEOS-Chem driver program <tt>main.f</tt>, we have moved the following calls to diagnostic subroutines:
 
In GEOS-Chem driver program <tt>main.f</tt>, we have moved the following calls to diagnostic subroutines:
Line 171: Line 133:
  
 
=== The impact of the reordering of the diagnostics ===
 
=== The impact of the reordering of the diagnostics ===
 +
 +
<span style="color:darkorange">'''''NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.'''''</span>
  
 
In [[GEOS-Chem versions under development#v8-01-02|GEOS-Chem v8-01-02]] and earlier releases, the order of operations as called from the <tt>main.f</tt> driver program was as follows:
 
In [[GEOS-Chem versions under development#v8-01-02|GEOS-Chem v8-01-02]] and earlier releases, the order of operations as called from the <tt>main.f</tt> driver program was as follows:

Latest revision as of 17:38, 15 November 2017

Overview

BETA RELEASE December 2008

What's new in this version

Contains everything in v8-01-02 plus the following updates:

Previous issues now resolved in v8-01-03

TPCORE replaced with version based on GMI model

Please see the discussion on our TPCORE wiki page about the implementation of the GMI version of TPCORE into GEOS-Chem.

Also see this PDF document for more information about the new TPCORE version as installed in GEOS-Chem v8-01-03.

--Bob Y. 09:42, 17 February 2010 (EST)

Output of ND51 does not match output in the ctm.bpch file

NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.

Claire Carouge wrote:

I found the problem [that Prasad Kasibhatla had reported] between ctm.bpch and ts_satellite.bpch. In fact for ND51, a variable is declared with a wrong type. So in diag51_mod.f you need to replace these lines :
     ! Local variables 
     INTEGER :: I, LT
by these:
     ! Local variables 
     INTEGER :: I
     REAL*8  :: LT
Doing so, I only get errors smaller than 5e-5 % between ctm.bpch and ts_satellite.bpch.

--Bob Y. 14:01, 15 December 2008 (EST)

ND22 (J-value) diagnostic

NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.

A problem was discovered in the ND22 diagnostic. If you typed the following in the diagnostic section of the input.geos file:

ND22: J-Values          : 47   all             
      => JV time range  :      11 13

then this was fine. However, if you requested a subset of tracers, then you would not get the correct number of tracers printed out.

Claire Carouge and Bob Yantosca have implemented a fix into diag3.f such that there is now a test for the name of each tracer. As a side-effect of this fix, you may no longer type all into the input.geos file. You must explicitly list each tracer number. For example, you may type:

ND22: J-Values          : 47   1 7 8 20 99              
      => JV time range  :      11 13

where tracers #1, #7, #8, #20 will cause J(NO2), J(HNO3), J(H2O2) and J(CH2O) (respectively) to be archived to the diagnostics. Tracer #99 will cause both J(OH) and J(O3) (which is really J(O1D)) to be archived.

--Bob Y. 15:53, 15 December 2008 (EST)

ND34 (biofuel emissions) diagnostic

NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.

Prasad Kasibhatla pointed out an inconsistency in the biofuel emissions diagnostics ND29 (slot #3) and ND34. There was a problem in the writing of ND34 when asking for a subset of tracers only. The code doesn't write out the array parts corresponding to the tracers asked for.

To fix it, you need to change the line in diag3.f

           ARRAY(:,:,1) = AD34(:,:,N) / SCALESRCE

by:

           DO MM = 1, NBFTRACE
              IF ( BFTRACE(MM) == NN ) THEN
                 MMB = MM
                 EXIT
              ENDIF
           ENDDO

           ARRAY(:,:,1) = AD34(:,:,MMB) / SCALESRCE

Also as a side-effect of this fix, you must explicitly declare the tracer numbers for which you wish to archive biofuel emissions. For example, use this line in input.geos:

ND34: Biofuel emissions :  1   1 4 5 9 10 11 18 19 20 21

--Bob Y. 16:01, 15 December 2008 (EST)

Change of location of calls to diagnostics in main.f

DIAG_2PM

NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.

We have moved the call to subroutine DIAG_2PM to after the call to subroutine INTERP. This will ensure that the correct value of tropopause pressure (TROPP) will be obtained for GEOS-4 met fields.

NOTE: For GEOS-5, the TROPP field is a 3-hour average and not and instantaneous field, so this move should have no effect.

--Bob Y. 16:18, 15 December 2008 (EST)

DIAG1, DIAG41, DIAG42

NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.

In GEOS-Chem driver program main.f, we have moved the following calls to diagnostic subroutines:

        !==============================================================
        !       ***** A R C H I V E   D I A G N O S T I C S *****
        !==============================================================
        IF ( ITS_TIME_FOR_DYN() ) THEN

           ! Accumulate several diagnostic quantities
           CALL DIAG1

           ! ND41: save PBL height in 1200-1600 LT (amf)
           ! (for comparison w/ Holzworth, 1967)
           IF ( ND41 > 0 ) CALL DIAG41

           ! ND42: SOA concentrations [ug/m3]
           IF ( ND42 > 0 ) CALL DIAG42

           !### Debug
           IF ( LPRT ) CALL DEBUG_MSG( '### MAIN: a DIAGNOSTICS' )
        ENDIF

from after transport to after wet deposition. This was to remove some historical baggage, and to make the ctm.bpch diagnostics more consistent with the ND48, ND49, ND50, ND51 timeseries diagnostics.

The impact of the reordering of the diagnostics

NOTE: We are phasing out binary punch diagnostics output, in favor of netCDF output.

In GEOS-Chem v8-01-02 and earlier releases, the order of operations as called from the main.f driver program was as follows:

  1. Advection (i.e. TPCORE)
  2. PBL mixing
  3. Cloud convection
  4. MONTHLY or DAILY MEAN DIAGNOSTICS (i.e. DIAG1, DIAG41, DIAG42)
  5. Dry Deposition
  6. Emissions
  7. Chemistry
  8. Wet Deposition
  9. TIMESERIES DIAGNOSTICS (i.e. ND48, ND49, ND50, ND51)

Subroutine DIAG1 is the main accumulator for several of the monthly or daily mean diagnostics (e.g. tracer concentrations, surface pressure, etc.) in ctm.bpch. DIAG41 archives afternoon PBL heights and DIAG42 archives SOA concentrations (these were added later).

Due to historical reasons, the call to DIAG1 (as well as later-added routines DIAG41 and DIAG42) had been placed the cloud convection. However, as the code developed and timeseries diagnostics (ND48, ND49, ND50, ND51) were incorporated into GEOS-Chem, these timeseries diagnostics were called after chemistry and wet deposition.

A couple of users have pointed out that the MONTHLY or DAILY MEAN diagnostics were not consistent with the TIMESERIES DIAGNOSTICS because they are called from different points within the main driver program. Therefore, in order to improve consistency between these all diagnostics, we now call the MONTHLY or DAILY MEAN DIAGNOSTICS (e.g. DIAG1, DIAG41, DIAG2) after chemistry and wet deposition.

Therefore, in GEOS-Chem v8-01-03, the new order of operations is as follows:

  1. Advection (i.e. TPCORE)
  2. PBL mixing
  3. Cloud convection
  4. Dry Deposition
  5. Emissions
  6. Chemistry
  7. Wet Deposition
  8. MONTHLY or DAILY MEAN DIAGNOSTICS (i.e. DIAG1, DIAG41, DIAG42)
  9. TIMESERIES DIAGNOSTICS (i.e. ND48, ND49, ND50, ND51)

NOTE: The switch in diagnostic location may result in some changes in tracer concentration as compared to previous versions of GEOS-Chem. This may especially be true for the dust and seasalt tracers.

--Bob Y. 11:04, 6 May 2009 (EDT)