GEOS-Chem Nested Model: Difference between revisions

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All users interested in the GEOS-Chem regional air quality simulations (e.g. nested-grid, GEOS-Chem/CMAQ linkages, etc.) are encouraged to subscribe to the regional air quality email list (click on the link in the [[#Contact information|contact information section]] below).
This page provides information for users interested in the GEOS-Chem nested grid simulations.


== Contact information ==
== Contact information ==
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{| border=1 cellspacing=0 cellpadding=5
{| border=1 cellspacing=0 cellpadding=5
|-valign="top"
|-valign="top"
!width="300px" bgcolor="#CCCCCC"|Nested Model Working Group Co-Chairs
!width="300px" bgcolor="#CCCCCC"|Nested Model Scientist
|width="600px"|
|width="600px"|
*[http://www.uh.edu/nsm/earth-atmospheric/people/faculty/yuxuan-wang/ Yuxuan Wang]
*[http://www.atmos.pku.edu.cn/lzhang/ Lin Zhang]
*[http://www.atmos.pku.edu.cn/lzhang/ Lin Zhang]


|-valign="top"
!bgcolor="#CCCCCC"|Nested Model Working Group email list
|<tt>geos-chem-regional [at] g.harvard.edu</tt>
|-valign="top"
!bgcolor="#CCCCCC"|To subscribe to email list
|Either
*Send an email to <tt>geos-chem-regional+subscribe [at] g.harvard.edu</tt>
Or
*Go to [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-regional GEOS-Chem Nested Model Google Group]
*Click on '''Subscribe to this group'''
|-valign="top"
!bgcolor="#CCCCCC"|To unsubscribe from email list
|Either
*Send an email to <tt>geos-chem-regional+unsubscribe [at] g.harvard.edu</tt>
Or
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-regional GEOS-Chem Nested Model Google Group]
*Click on the '''My Settings''' button
*Click on '''Leave this group'''
|}
|}
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:32, 21 August 2015 (UTC)


== Current Regional Working Group Projects (Please add yours!) ==
== Current Regional Working Group Projects (Please add yours!) ==
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|US EPA
|US EPA
|Develop Boundary Conditions for USA Regional Chemical Transport Models for 2015 and 2016
|Develop Boundary Conditions for USA Regional Chemical Transport Models for 2015 and 2016
|
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]
|-
|Dalhousie U.
|Develop stretched grid for GCHP
|
|[mailto:liam.bindle@dal.ca Liam Bindle]
|}
|}
== Recent updates to nested GEOS-Chem ==
=== Fixes to Streets emissions for model years 2005 and earlier ===
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03f|v9-01-03f]] and approved on 17 Feb 2012.'''''
We discovered two bugs in the implementation of Streets emissions for the nested model. These will affect all nested simulations at least through v9-01-02 for model years 2005 and earlier.
1. The nested model was using Streets 2000 emissions for years 2001-2005 instead of Streets 2006 emissions, which the global model has been using since v8-03-01. This will be updated in [[GEOS-Chem v9-01-03]].
2. Streets 2000 anthropogenic emissions include NOx, CO, and SO2 from ships, which leads to double-counting of ship emissions as well as improper treatment of NOx emissions. This problem is described in more detail on the [[Ship_emissions#Duplicate_ship_emissions_in_Asia_in_Streets_2000_inventory | ship emissions page]]. This will be updated in [[GEOS-Chem v9-01-03]].
--Jenny Fisher, 1 February 2012


=== Nested-grid capability for offline simulations ===
=== Nested-grid capability for offline simulations ===
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|[[CO2 simulation#Nested-grid CO2 simulation|Nested-grid CO2 simulation]]
|[[CO2 simulation#Nested-grid CO2 simulation|Nested-grid CO2 simulation]]
|Yuxuan Wang (Tsinghua U.)
|Yuxuan Wang (Tsinghua U.)
|Added to [[GEOS-Chem v9-01-03]]; released 14 Sep 2012
|Added to [[GEOS-Chem v9-01-03]]
|-
|-
|[[CH4 simulation#Update methane emissions and add capability for North America nested grid|CH4 simulation]] (North America)
|[[CH4 simulation#Update methane emissions and add capability for North America nested grid|CH4 simulation]] (North America)
|Kevin Wecht (Harvard)
|Kevin Wecht (Harvard)
|Added to [[GEOS-Chem v9-01-03]]; released 14 Sep 2012
|Added to [[GEOS-Chem v9-01-03]]
|-
|-
|[[Mercury#Nested-grid Hg simulation over North_America|Hg simulation]] (North America)
|[[Mercury#Nested-grid Hg simulation over North_America|Hg simulation]] (North America)
|Yanxu Zhang (U. Washington)
|Yanxu Zhang (U. Washington)
|Slated for inclusion into [[GEOS-Chem v9-02]]
|Added to [[GEOS-Chem v9-02]]
|}
|}


--[[User:Bmy|Bob Y.]] 16:42, 14 September 2012 (EDT)
== Further reading ==
 
===Nested grid model at 0.25&deg; x 0.3125&deg; resolution using GEOS-FP===
 
====North America region====
 
=====Developers=====
*Patrick Kim (Harvard)
*Lei Zhu (Harvard)
*Karen Yu (Harvard)
*Katie Travis (Harvard)
*Jenny Fisher (U. Wollongong)
 
=====Overview=====
 
The 0.25&deg; x 0.3125&deg; nested-grid simulation over North America was implemented in [[GEOS-Chem v9-02]]. Data for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_NA GEOS-FP 0.25&deg; x 0.3125&deg; North America nested grid] can be downloaded from the Harvard or Dalhousie data archives via FTP. Please see our [[Available_met_data_for_nested_grid_simulations#GEOS-FP_2|''Available met data for nested grid simulations'' wiki page]] for more information.
 
====China region====
 
=====Developers=====
*Patrick Kim (Harvard)
*Libao Chai (Tsinghua)
*Yu Yao (Tsinghua)
*Yuxuan Wang ((Tsinghua and Texas A&M Galveston)
*Lin Zhang (Peking University)
 
=====Overview=====
 
Data for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_CH GEOS-FP 0.25&deg; x 0.3125&deg; China nested grid] can be downloaded from the Dalhousie data archives via FTP. Please see our [[Available_met_data_for_nested_grid_simulations#GEOS-FP|''Available met data for nested grid simulations'' wiki page]] for more information.
 
=====Bug fixes for the 0.25 x 0.3125 nested CH simulation=====
 
'''''These updates were validated with the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01f|v10-01f]] and approved on Approved 13 Jan 2015.'''''
 
'''''Yuxuan Wang wrote:'''''
 
:I’m happy to report that we’ve finally implemented all the bug fixes and necessary input files to successfully run the 0.25 nested_CH full chemistry simulation on the Tsinghua platform. We’ve done a 10-day test run and the simulation results look reasonable, so I thought it’s a good time to submit our code updates to the GC Support Team so that they can be incorporated in the next code release.
:[http://wiki.seas.harvard.edu/geos-chem/images/Bug_fix_NEST_CH_025.txt Attached] please find a summary list of the code fixes we’ve implemented on the basis of v9-02 public release.  The codes and input data are located at ftp://166.111.42.70/share/v9-02_CH025/.
 
--[[User:Melissa Payer|Melissa Sulprizio]] 15:07, 18 November 2014 (EST)
 
====Europe region====
 
=====Developers=====
*Junwei Xu (Dalhhousie)
*Anna Protonatariou (Athens)
 
=====Overview=====
 
Data for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_EU GEOS-FP 0.25&deg; x 0.3125&deg; Europe nested grid] can be downloaded from the Dalhousie data archives via FTP. Please see our [[Available_met_data_for_nested_grid_simulations#GEOS-FP_3|''Available met data for nested grid simulations'' wiki page]] for more information.
 
=====Bug fixes for the 0.25 x 0.3125 nested EU simulation=====
 
<span style="color:green">'''''These fixes were included in the [[GEOS-Chem v10-01#Fixes and updates added during the public comment period|GEOS-Chem v10-01 public release]].'''''</span>
 
'''''Anna Protonatariou wrote:'''''
 
:1. I updated the Headers/CMN_SIZE_mod.F to define IGLOB, JGLOB for the European region at 0.25x0.3125 resolution by adding similar code as for CH and NA. The correct numbers are:
 
      INTEGER            :: IGLOB      = 177
      INTEGER            :: JGLOB      = 115
 
:2. Then I got another compilation error in strat_chem_mod.F90
 
:A. I found that the problem was in line 1613, which was only for CH and NA:
 
  #if defined( NESTED_CH ) || defined( NESTED_NA )
 
:So I  added the European part and now it is:
 
  #if defined( NESTED_CH ) || defined( NESTED_NA )|| defined(NESTED_EU)
 
:B. Lines 1603-1609 were:
 
  #elif defined( GRID025x03125 )
  #if defined( NESTED_CH )
      INTEGER, PARAMETER  :: J30S = 1, J30N = 161
  #elif defined( NESTED_NA )
      INTEGER, PARAMETER  :: J30S = 1, J30N = 161
  #endif
 
:I added the European part and now it is :
 
  #elif defined( GRID025x03125 )
  #if defined( NESTED_CH )
      INTEGER, PARAMETER  :: J30S = 1, J30N = 161
  #elif defined( NESTED_NA )
      INTEGER, PARAMETER  :: J30S = 1, J30N = 161
  #elif defined( NESTED_EU )
      INTEGER, PARAMETER  :: J30S = 1, J30N = 115
  #endif
 
:However, I think NA should be 202 and not 161 (which is the grid number for CH)!
 
:Compilation is now successfully ended!! So happy with that:) I send you attached the routines. Unfortunately I get errors when I tried to run the model.
 
Anna is following up with the Nested Model Working Group to resolve issues encountered while trying to run the 0.25&deg; x 0.3125&deg;  European nested grid simulation. Development is ongoing.
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:45, 20 May 2015 (UTC)
 
== Recent linking tool updates for GEOS-Chem and CMAQ ==
 
 
== On-going Developments ==
 
'''[[##lists|1. Modified for Code.v8-02-01]]'''
 
1). main.f, add following lines after DO_CHEMISTRY in line 941:
<pre>
        ! check STT (yxw) 
#if  defined( GEOS_5 ) && defined( GRID05x0666 )
            ! Loop over grid boxes
!$OMP PARALLEL DO
!$OMP+DEFAULT( SHARED )
!$OMP+PRIVATE( I, J, L, N )
            DO N = 1, N_TRACERS
            DO L = 1, LLPAR
            DO J = 1, JJPAR
            DO I = 1, IIPAR
              !---------------------------
              ! Check for Negatives
              !---------------------------
              IF ( STT(I,J,L,N) < 0d0 ) THEN
!$OMP CRITICAL
                  WRITE( 6, 100 ) I, J, L, N, STT(I,J,L,N)
                  PRINT*, 'Neg STT after chemistry ' //
    &                  'SET STT TO BE ZERO'
                  STT(I,J,L,N) = 0d0
!$OMP END CRITICAL
              !---------------------------
              ! Check for NaN's
              !---------------------------
              ELSE IF ( IT_IS_NAN( STT(I,J,L,N) ) ) THEN
!$OMP CRITICAL
                  WRITE( 6, 100 ) I, J, L, N, STT(I,J,L,N)
                  PRINT*, 'NaN STT after chemistry ' //
    &                  'SET STT TO BE LOWER LEVEL'
                  STT(I,J,L,N) = STT(I,J,L-1,N)
!$OMP END CRITICAL
              !----------------------------
              ! Check STT's for Infinities
              !----------------------------
              ELSE IF ( .not. IT_IS_FINITE( STT(I,J,L,N) ) ) THEN
!$OMP CRITICAL
                  WRITE( 6, 100 ) I, J, L, N, STT(I,J,L,N)
                  PRINT*, 'Inf STT after chemistry ' //
    &                  'SET STT TO BE LOWER LEVEL'
                  STT(I,J,L,N) =  STT(I,J,L-1,N)
!$OMP END CRITICAL           
 
              ENDIF
            ENDDO
            ENDDO
            ENDDO
            ENDDO
!$OMP END PARALLEL DO
#endif
</pre>
 
2). main.f, add following lines after ITS_TIME_FOR_DIAG  in line 1021:
<pre>
        ! Sometimes STT in the stratosphere can be negative at
        ! the nested-grid domain edges. Force them to be zero before
        ! CHECK_STT (yxw)
#if  defined( GEOS_5 ) && defined( GRID05x0666 )
            ! Loop over grid boxes
!$OMP PARALLEL DO
!$OMP+DEFAULT( SHARED )
!$OMP+PRIVATE( I, J, L, N )
            DO N = 1, N_TRACERS
            DO L = 1, LLPAR
            DO J = 1, JJPAR
            DO I = 1, IIPAR
 
              !---------------------------
              ! Check for Negatives
              !---------------------------
              IF ( STT(I,J,L,N) < 0d0 ) THEN
!$OMP CRITICAL
                  WRITE( 6, 100 ) I, J, L, N, STT(I,J,L,N)
                  PRINT*, 'Neg STT after dynamics step ' //
    &            'SET STT TO BE ZERO'
                  STT(I,J,L,N) = 0d0
!$OMP END CRITICAL
              ENDIF
            ENDDO
            ENDDO
            ENDDO
            ENDDO
!$OMP END PARALLEL DO
100  FORMAT( ' STT(',i3,',',i3,',',i3,',',i3,') = ', f13.6 )
 
#endif
 
</pre>
 
--[[User:Yuxuan|Wang]],[[User:Dan|Chen]], 05:13, 25 June 2009 (EDT)
--[[User:Aaron van Donkelaar], March 4, 2010
 
== How to run the 0.5x0.667 nested-grid for GEOS-5 ==
 
We have moved this discussion to the following wiki pages:


#[[GEOS-Chem nested grid simulations]]  
*[[GEOS-Chem nested grid simulations]]  
#[[Setting up GEOS-Chem nested grid simulations]]
*[[Setting_up_GEOS-Chem_nested_grid_simulations#GEOS-Chem_12.4.0_and_later|Setting up nested grid simulations in GEOS-Chem 12.4.0 and later]]
*[[Setting_up_GEOS-Chem_nested_grid_simulations#GEOS-Chem_12.3.2_and_earlier|Setting up nested grid simulations in GEOS-Chem 12.3.2 and earlier]]


--[[User:Bmy|Bob Y.]] 14:07, 15 November 2010 (EST)
== Two-way coupling between global and nested GEOS-Chem models ==


== About linking tools ==
For those who are interested in two-way coupling between global and nested GEOS-Chem models, including setups, see [[Two-way coupling between global and nested GEOS-Chem models]]


TBD
--[[User:jackylinq|Jintai Lin]] 22:15, 23 February 2018 (BJT)

Latest revision as of 11:44, 6 September 2024

This page provides information for users interested in the GEOS-Chem nested grid simulations.

Contact information

Nested Model Scientist

Current Regional Working Group Projects (Please add yours!)

User Group Description Funding Contact Person
Tsinghua Nested-grid GEOS-Chem model development; Regional air quality over East Asia and interactions with the globe N/A Yuxuan Wang
SNU Regional PM simulations over East Asia Ministry of Environment in Korea Rokjin Park
US EPA N/A Rob Pinder
U. Tennessee N/A Joshua Fu
Nat'l Obs. Athens N/A Anna Protonotariou
U. L'Aquila Buondary conditions to CHIMERE model over Europe, focus on Saharan dust transport. ASI (Italian Space Agency) Gabriele Curci
Georgia Tech. N/A Tao Zeng
U. Toronto N/A Jane Liu
Peking University Regional air quality in East Asia, Inversion of trace gas emissions using satellite products N/A May Fu
Dalhousie U. Surface PM2.5 retrieval using satellite products N/A Aaron van Donkelaar
Dalhousie U. Nested aerosol microphysics (TOMAS). NOx/ultrafine aerosol concentration relationships. Topographic influence on microphysics N/A Jeffrey Pierce
SUNY-Albany Regional particle formation, evolution, and properties: Nested-grid GEOS-Chem (with APM) simulations and comparisons with measurements Fangqun Yu
U. Edinburgh Quantify the impact of boreal biomass burning outflow on tropospheric chemistry over the North Atlantic: Nested grid simulations and evaluation with ground-based, aircraft, and satellite observations Mark Parrington
Emory University Improving MISR Aerosol retrieval with GEOS-Chem simulated aerosol composition NASA Yang Liu
Peking University Carbonaceous aerosols in China May Fu
Peking University Two-way nesting model for GESO-Chem and impacts on regional air quality and long-range transport Jintai Lin
CSU Investigation of inorganic aerosol and role of NH3 during CalNex Luke Schiferl
University of Wollongong Nested grid for Australia L'Oréal-UNESCO Jenny Fisher
Harvard Variability of HCHO Over the Southeastern United States Observed from Space NASA AQAST Lei Zhu
UNL GEOS-Chem Satellite Simulator for future sensors NASA Jun Wang
Harvard, York, CSU Develop 0.5° x 0.67° grid for continental Africa (Eloise) and 0.25° x 0.3125° grid for West Africa (Mat, Eleanor, Daven) Eloise Marais, Mat Evans, Eleanor Morris Daven Henze
Purdue Develop 0.5° x 0.67° grid for the Arctic Zeli Tan
Peking University Regional ozone and PM pollution over Asia; Develop 0.25 x 0.3125 degree simulation in the adjoint model Lin Zhang
University of York Evaluation of the GC European grid for AQ applications Mat Evans Tim Garstin
US EPA Develop Boundary Conditions for USA Regional Chemical Transport Models for 2015 and 2016 Barron H. Henderson
Dalhousie U. Develop stretched grid for GCHP Liam Bindle

Nested-grid capability for offline simulations

The following offline simulations have been updated for the nested grid:

Simulation Author Status
Nested-grid CO2 simulation Yuxuan Wang (Tsinghua U.) Added to GEOS-Chem v9-01-03
CH4 simulation (North America) Kevin Wecht (Harvard) Added to GEOS-Chem v9-01-03
Hg simulation (North America) Yanxu Zhang (U. Washington) Added to GEOS-Chem v9-02

Further reading

Two-way coupling between global and nested GEOS-Chem models

For those who are interested in two-way coupling between global and nested GEOS-Chem models, including setups, see Two-way coupling between global and nested GEOS-Chem models

--Jintai Lin 22:15, 23 February 2018 (BJT)

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