GEOS-Chem Adjoint v34: Difference between revisions

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|[[#Add_support_for_RETRO_emissions |Add support for RETRO emissions]]
|[[#Add_support_for_RETRO_emissions |Add support for RETRO emissions]]
|Forward Model Update
|Forward Model Update
|Melissa Payer
|Wes Reinhart (U. Minnesota), Dylan Millet (U. Minnesota)
|Yanko Davila (CU Boulder)
|Yanko Davila (CU Boulder)
|v34e
|v34e
Line 161: Line 161:
|Approved 12 Mar 2013
|Approved 12 Mar 2013
|-bgcolor="#CCFFFF"
|-bgcolor="#CCFFFF"
|-
|[[#Added_support_for_off-diagonal_covariance | Added support for off-diagonal covariance]]
|Adjoint Model Update
|Nicolas Bousserez (CU Boulder)
|Yanko Davila (CU Boulder)
|v34f
|Approved 4 Apr 2013
|-bgcolor="#CCFFFF"
|-
|[[#Nested_Transport_Fix | Nested Transport Fix]]
|Forward Model Bug Fix
|Lin Zhang (Harvard)
|Yanko Davila (CU Boulder)
|v34g
|Approved 4 Apr 2013
|-bgcolor="#CCFFFF"
|-
|[[#Bug_fix_for_mass_transport_flux_diagnostics | Bug fix for mass transport flux diagnostics]]
|Forward Model Bug Fix
|Mat Evans
|Yanko Davila (CU Boulder)
|v34h
|Approved 17 Apr 2013
|-bgcolor="#CCFFFF"
|-
|[[#Bug_fix_in_streets_anthro_mod.F_for_offline_simulations | Bug fix in streets_anthro_mod.F for offline simulations]]
|Forward Model Bug Fix
|Fabien Paulot
|Yanko Davila (CU Boulder)
|v34h
|Approved 17 Apr 2013
|-bgcolor="#CCFFFF"
|-
|[[#Added_support_for_ISOROPIA_II | Added support for ISOROPIA II ]]
|Adjoint Model Update
|Shannon Capps (EPA), Daven Henze (CU Boulder)
|Yanko Davila (CU Boulder)
|v34i
|Approved 19 Apr 2013
|-bgcolor="#CCFFFF
|-
|[[#Diurnal_NOx_and_regional_biofuel_emissions_fix | Diurnal NOx and regional biofuel emissions fix ]]
|Forward Model Bug Fix
|Christoph Keller
|Yanko Davila (CU Boulder)
|v34j
|Approved 14 May 2013
|-bgcolor="#CCFFFF
|-
|[[#Fix_for_isoprene_nitrates_in_globchem.dat | Fix for isoprene nitrates in globchem.dat ]]
|Forward Model Bug Fix
|Fabien Paulot
|Yanko Davila (CU Boulder)
|v34k
|Approved 15 May 2013
|-bgcolor="#CCFFFF
-
|[[#Added_support_for_reaction_rate_constants_defined_in_input.gcadj | Added support for reaction rate constants defined in input.gcadj ]]
|Adjoint Model Update
|Hyunmin Lee (CU Boulder), Daven Henze (CU Boulder)
|Yanko Davila (CU Boulder)
|v34m
|Approved 25 June 2013
|-bgcolor="#CCFFFF
-
|[[#Updated_GMI_database | Updated GMI database ]]
|Forward Model Update
|Hyunmin Lee (CU Boulder), Daven Henze (CU Boulder)
|Yanko Davila (CU Boulder)
|v34n
|Approved 3 July 2013
|-bgcolor="#CCFFFF


|}
|}
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===== Add support for RETRO emissions =====
===== Add support for RETRO emissions =====


Added support for RETRO emissions.
Added support for [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02k | RETRO emissions.]]


See Benchmarks results [https://docs.google.com/spreadsheet/ccc?key=0As2MewHKyWpDdDlTeFdPanU2RzlWc0luaFpEQXlyclE#gid=0 gcadj_std_v34e test 001]
See Benchmarks results [https://docs.google.com/spreadsheet/ccc?key=0As2MewHKyWpDdDlTeFdPanU2RzlWc0luaFpEQXlyclE#gid=0 gcadj_std_v34e test 001]


--[[User:Yanko|Yanko]] 14:14, 14 March 2013 (EDT)
--[[User:Yanko|Yanko]] 14:14, 14 March 2013 (EDT)
===== Updated GMI database =====
Now we are using the same GMI data inventory as GEOS-Chem forward model [http://wiki.seas.harvard.edu/geos-chem/index.php/Stratospheric_chemistry#New_implementation_of_linearized_stratospheric_chemistry v9-01-03o].
With the adjoint model, one can calculate the sensitivities with respect to production and loss rates of [http://wiki.seas.harvard.edu/geos-chem/index.php/Stratospheric_chemistry#Original_Species 24 original species].
Note that the GEOS-Chem adjoint does not support Bromine chemistry yet.
--[[User:Hyung-Min Lee|Hyung-Min Lee]] 19:01, 3 July 2013 (EDT)
See Benchmarks results [https://docs.google.com/spreadsheet/ccc?key=0As2MewHKyWpDdDlTeFdPanU2RzlWc0luaFpEQXlyclE#gid=1 gcadj_std_v34n ]
--[[User:Yanko|Yanko]] 17:37, 3 July 2013 (EDT)


==== - Bug fixes in forward model ====
==== - Bug fixes in forward model ====
Line 206: Line 300:


--[[User:Yanko|Yanko]] 16:00, 4 March 2013 (EST)
--[[User:Yanko|Yanko]] 16:00, 4 March 2013 (EST)


=====  Bug fixes for biofuel emissions  =====  
=====  Bug fixes for biofuel emissions  =====  
Line 226: Line 319:
Ship NOx emissions are supposed to be emitted as (1 mol HNO3 + 10 mol O3) per mol NOx in the inventory. The code previously used molar masses incorrectly so that the ratios were actually 0.73 mol HNO3 and 9.5 mol O3. Thus, this bug fix will slightly increase O3 and HNO3 over the oceans. [[Ship_emissions#Bug_in_ship_NOx_emissions | See forward wiki. ]]
Ship NOx emissions are supposed to be emitted as (1 mol HNO3 + 10 mol O3) per mol NOx in the inventory. The code previously used molar masses incorrectly so that the ratios were actually 0.73 mol HNO3 and 9.5 mol O3. Thus, this bug fix will slightly increase O3 and HNO3 over the oceans. [[Ship_emissions#Bug_in_ship_NOx_emissions | See forward wiki. ]]


See Benchmarks results [https://docs.google.com/spreadsheet/ccc?key=0As2MewHKyWpDdDlTeFdPanU2RzlWc0luaFpEQXlyclE#gid=0 gcadj_std_v34e test 003 to 008]
--[[User:Yanko|Yanko]] 19:43, 13 March 2013 (EDT)
 
=====  Nested Transport Fix =====
 
Applied a bug fix that affects transport for nested simulations with GEOS-5 met fields. [[Setting_up_GEOS-Chem_nested_grid_simulations#Transport_fix | See forward wiki. ]]
 
--[[User:Yanko|Yanko]] 18:59, 4 April 2013 (EDT)
 
=====  Bug fix for mass transport flux diagnostics =====
 
Applied a bug fix to LD24,LD25and LD25 diagnostics. [[GEOS-Chem_v9-01-03#Bug_fix_for_mass_transport_flux_diagnostics | See forward wiki. ]]
 
--[[User:Yanko|Yanko]] 15:27, 17 April 2013 (EDT)
 
=====  Bug fix in streets_anthro_mod.F for offline simulations =====
 
Applied a bug fix to avoid issues with the offline chemistry where idtnh3 is not equal to 30. [[GEOS-Chem_v9-01-03#Bug_fix_in_streets_anthro_mod.F_for_offline_simulations | See forward wiki. ]]
 
--[[User:Yanko|Yanko]] 15:27, 17 April 2013 (EDT)
 
=====  Diurnal NOx and regional biofuel emissions fix =====
 
Diurnal NOx scale factors should be based on UTC instead of local time. Also we currently double count biofuel emissions over Canada and Mexico if the respective local inventories (CAC and BRAVO) are used. [[GEOS-Chem_v9-02#Bug_fixes_in_biofuel_mod.F_and_emfossil.F | See forward wiki. ]]
 
See Benchmarks results [https://docs.google.com/spreadsheet/ccc?key=0As2MewHKyWpDdDlTeFdPanU2RzlWc0luaFpEQXlyclE#gid=0 gcadj_std_v34j test 001]
 
--[[User:Yanko|Yanko]] 13:07, 15 May 2013 (EDT)
 
=====  Fix for isoprene nitrates in globchem.dat =====
 
Fabien Paulot discovered an error in the reaction for isoprene nitrates in globchem.dat for the SOA and standard simulations. [[GEOS-Chem_v8-03-02#Fix_for_isoprene_nitrates_in_globchem.dat | See forward wiki. ]]
 
See Benchmarks results [https://docs.google.com/spreadsheet/ccc?key=0As2MewHKyWpDdDlTeFdPanU2RzlWc0luaFpEQXlyclE#gid=0 gcadj_std_v34k test 001]
 
--[[User:Yanko|Yanko]] 15:49, 15 May 2013 (EDT)
 


--[[User:Yanko|Yanko]] 19:43, 13 March 2013 (EDT)


==== - Updates to adjoint model ====
==== - Updates to adjoint model ====
Line 257: Line 384:


--[[User:Yanko|Yanko]] 19:06, 14 November 2012 (EST)
--[[User:Yanko|Yanko]] 19:06, 14 November 2012 (EST)
=====  Added support for off-diagonal covariance =====
- Now possibility to define correlations (off-diagonal terms) in the background (prior) covariance error matrix. User can define the latitude and longitude correlation length in input.gcadj. See Singh et al. (2011): Construction of non-diagonal background error covariance matrices for global chemical data assimilation, Geosci. Model Dev. ,4, 299-316 for more information.
See Benchmarks results [https://docs.google.com/spreadsheet/ccc?key=0As2MewHKyWpDdDlTeFdPanU2RzlWc0luaFpEQXlyclE#gid=0 gcadj_std_v34f test 003 to 005]
--[[User:Yanko|Yanko]] 17:38, 4 April 2013 (EDT)
=====  Added support for ISOROPIA II =====
- The ISORROPIA II package performs aerosol thermodynamical equilibrium. It partitions nitrate (HNO3 and NIT) and ammonia (NH3 and NH4) between the gas and aerosol phases. Inputs to the partitioning routine include temperature and RH. ISORROPIA II has significant benefits over previous implementations of ISORROPIA, especially for partitioning of nitrate at low RH. [[ ISORROPIA_II | Click here more information. ]]
See Benchmarks results [https://docs.google.com/spreadsheet/ccc?key=0As2MewHKyWpDdDlTeFdPanU2RzlWc0luaFpEQXlyclE#gid=0 gcadj_std_v34i test 003 to 005]
--[[User:Yanko|Yanko]] 12:19, 22 April 2013 (EDT)
===== Added support for reaction rate constants defined in input.gcadj =====
- Reaction rate constants can now be selected as control variables for sensitivity analysis or optimization.  The complete set of reaction rate constants, or subsets, can be specified in input.gcadj.
See Benchmarks results [https://docs.google.com/spreadsheet/ccc?key=0As2MewHKyWpDdDlTeFdPanU2RzlWc0luaFpEQXlyclE#gid=0 gcadj_std_v34m test 001 to 011]
--[[User:Yanko|Yanko]] 17:38, 25 June 2013 (EDT)


==== - Bug fixes in adjoint model ====
==== - Bug fixes in adjoint model ====

Latest revision as of 21:27, 24 July 2013

Overview

BETA RELEASE

What's new in this version

GEOS-Chem Adjoint v34 contains the following major updates and improvements.

- -
Feature Type Submitted by Committed by Version Status
Building Process Updated Adjoint Update Daven Henze (CU Boulder), Yanko Davila (CU Boulder) Yanko Davila (CU Boulder) v34 Approved 14 Nov 2012
Add support for GFED3 Emissions Forward Model Update Melissa Payer (Harvard) Yanko Davila (CU Boulder) v34 Approved 14 Nov 2012
Checkpoint files creation updated Adjoint Update Daven Henze (CU Boulder), Yanko Davila (CU Boulder) Yanko Davila (CU Boulder) v34 Approved 14 Nov 2012
population-weighted cost function updated Adjoint Update Daven Henze (CU Boulder) Yanko Davila (CU Boulder) v34 Approved 14 Nov 2012
Add support for GFED2 8day and 3hr Emissions Adjoint Update Daven Henze (CU Boulder), Yanko Davila (CU Boulder) Yanko Davila (CU Boulder) v34 Approved 14 Nov 2012
M undefined Adjoint Bug Fix Daven Henze (CU Boulder), Yanko Davila (CU Boulder) Yanko Davila (CU Boulder) v34 Approved 14 Nov 2012
Error compiling on ifort 12 Adjoint Bug Fix Yanko Davila (CU Boulder) Yanko Davila (CU Boulder) v34 Approved 14 Nov 2012
Set observation errors to 1% in pseudo-obs test Adjoint Bug Fix Nicolas Bousserez (CU Boulder) Yanko Davila (CU Boulder) v34a Approved 11 Dec 2012
Update to Nested Domains Forward Model Bug Fix Daven Henze (CU Boulder) Yanko Davila (CU Boulder) v34b Approved 25 Jan 2013
Fixed Makefile Bug Adjoint Bug Fix Yanko Davila (CU Boulder) Yanko Davila (CU Boulder) v34b Approved 25 Jan 2013
Added support for ICOADS ship emissions Forward Model Update Katerina Lapina (CU Boulder), Daven Henze (CU Boulder) Yanko Davila (CU Boulder) v34c Approved 5 Feb 2013
Washout fix for non-aerosol species Forward Model Bug Fix Helen Amos Yanko Davila (CU Boulder) v34d Approved 4 Mar 2013
Add support for RETRO emissions Forward Model Update Wes Reinhart (U. Minnesota), Dylan Millet (U. Minnesota) Yanko Davila (CU Boulder) v34e Approved 12 Mar 2013
Bug fixes for biofuel emissions Forward Model Bug Fix Melissa Payer Yanko Davila (CU Boulder) v34e Approved 12 Mar 2013
Fix bug in EDGAR ship emissions code Forward Model Bug Fix Michael Long Yanko Davila (CU Boulder) v34e Approved 12 Mar 2013
Bug fix for ship NOx emissions Forward Model Bug Fix Chris Holmes Yanko Davila (CU Boulder) v34e Approved 12 Mar 2013
Added support for off-diagonal covariance Adjoint Model Update Nicolas Bousserez (CU Boulder) Yanko Davila (CU Boulder) v34f Approved 4 Apr 2013
Nested Transport Fix Forward Model Bug Fix Lin Zhang (Harvard) Yanko Davila (CU Boulder) v34g Approved 4 Apr 2013
Bug fix for mass transport flux diagnostics Forward Model Bug Fix Mat Evans Yanko Davila (CU Boulder) v34h Approved 17 Apr 2013
Bug fix in streets_anthro_mod.F for offline simulations Forward Model Bug Fix Fabien Paulot Yanko Davila (CU Boulder) v34h Approved 17 Apr 2013
Added support for ISOROPIA II Adjoint Model Update Shannon Capps (EPA), Daven Henze (CU Boulder) Yanko Davila (CU Boulder) v34i Approved 19 Apr 2013
Diurnal NOx and regional biofuel emissions fix Forward Model Bug Fix Christoph Keller Yanko Davila (CU Boulder) v34j Approved 14 May 2013
Fix for isoprene nitrates in globchem.dat Forward Model Bug Fix Fabien Paulot Yanko Davila (CU Boulder) v34k Approved 15 May 2013
Added support for reaction rate constants defined in input.gcadj Adjoint Model Update Hyunmin Lee (CU Boulder), Daven Henze (CU Boulder) Yanko Davila (CU Boulder) v34m Approved 25 June 2013
Updated GMI database Forward Model Update Hyunmin Lee (CU Boulder), Daven Henze (CU Boulder) Yanko Davila (CU Boulder) v34n Approved 3 July 2013


- Updates to forward model

Add GFED3 Emissions

Implemented GFDE3 Emissions

See benchmark results gcadj_std_v34 tests 005 and 006

--Yanko 19:06, 14 November 2012 (EST)

Added support for ICOADS ship emissions

Added support for ICOADS ship emissions.

See Benchmarks results gcadj_std_v34c test 003

--Yanko 13:49, 5 February 2013 (EST)

Add support for RETRO emissions

Added support for RETRO emissions.

See Benchmarks results gcadj_std_v34e test 001

--Yanko 14:14, 14 March 2013 (EDT)

Updated GMI database

Now we are using the same GMI data inventory as GEOS-Chem forward model v9-01-03o. With the adjoint model, one can calculate the sensitivities with respect to production and loss rates of 24 original species. Note that the GEOS-Chem adjoint does not support Bromine chemistry yet.

--Hyung-Min Lee 19:01, 3 July 2013 (EDT)

See Benchmarks results gcadj_std_v34n

--Yanko 17:37, 3 July 2013 (EDT)


- Bug fixes in forward model

Update to Nested Domains

Improved nested simulations. STRAT_CHEM update for regrid GMI files to nested domain.

See Benchmarks results gcadj_std_v34b

--Yanko 15:53, 25 January 2013 (EST)

Washout fix for non-aerosol species

The Wet deposition algorithm was underestimating washout of non-aerosol species. See forward wiki.

--Yanko 16:00, 4 March 2013 (EST)

Bug fixes for biofuel emissions

Fix for double-counting of residential biofuel when using RETRO and fix in biofuel emissions using Streets inventory. See forward wiki.

--Yanko 19:43, 13 March 2013 (EDT)

Fix bug in EDGAR ship emissions code

GEOS-Chem default configuration uses the ICOADS ship emissions instead of the EDGAR ship emissions. However, we still pass EDGAR_CO_SHIP to routine COMPUTE_EDGAR_CO even if it is not allocated. See forward wiki.

See Benchmarks results gcadj_std_v34e test 003 to 008

--Yanko 19:43, 13 March 2013 (EDT)

Bug fix for ship NOx emissions

Ship NOx emissions are supposed to be emitted as (1 mol HNO3 + 10 mol O3) per mol NOx in the inventory. The code previously used molar masses incorrectly so that the ratios were actually 0.73 mol HNO3 and 9.5 mol O3. Thus, this bug fix will slightly increase O3 and HNO3 over the oceans. See forward wiki.

--Yanko 19:43, 13 March 2013 (EDT)

Nested Transport Fix

Applied a bug fix that affects transport for nested simulations with GEOS-5 met fields. See forward wiki.

--Yanko 18:59, 4 April 2013 (EDT)

Bug fix for mass transport flux diagnostics

Applied a bug fix to LD24,LD25and LD25 diagnostics. See forward wiki.

--Yanko 15:27, 17 April 2013 (EDT)

Bug fix in streets_anthro_mod.F for offline simulations

Applied a bug fix to avoid issues with the offline chemistry where idtnh3 is not equal to 30. See forward wiki.

--Yanko 15:27, 17 April 2013 (EDT)

Diurnal NOx and regional biofuel emissions fix

Diurnal NOx scale factors should be based on UTC instead of local time. Also we currently double count biofuel emissions over Canada and Mexico if the respective local inventories (CAC and BRAVO) are used. See forward wiki.

See Benchmarks results gcadj_std_v34j test 001

--Yanko 13:07, 15 May 2013 (EDT)

Fix for isoprene nitrates in globchem.dat

Fabien Paulot discovered an error in the reaction for isoprene nitrates in globchem.dat for the SOA and standard simulations. See forward wiki.

See Benchmarks results gcadj_std_v34k test 001

--Yanko 15:49, 15 May 2013 (EDT)


- Updates to adjoint model

Building Process Updated

Building process updated to match forward model. Find more information about changes on the run script on the User's Guide Section 2.4 Page 27

--Yanko 19:06, 14 November 2012 (EST)

Checkpoint files creation updated

Now *chk* files are not created at X=0. Checkpoint files are not created at X=2, 3 if performing a finite diference test.

--Yanko 19:06, 14 November 2012 (EST)

Population_mod Updated

population_mod.f updated.

--Yanko 19:06, 14 November 2012 (EST)

Fix GFED2 Emissions

Fixed an error when using GFED2 8Daily and 3Hr emissions, the error occurred when running backwards because the emissions were called twice.

See Benchmarks results gcadj_std_v34 tests 003 and 004

--Yanko 19:06, 14 November 2012 (EST)

Added support for off-diagonal covariance

- Now possibility to define correlations (off-diagonal terms) in the background (prior) covariance error matrix. User can define the latitude and longitude correlation length in input.gcadj. See Singh et al. (2011): Construction of non-diagonal background error covariance matrices for global chemical data assimilation, Geosci. Model Dev. ,4, 299-316 for more information.

See Benchmarks results gcadj_std_v34f test 003 to 005

--Yanko 17:38, 4 April 2013 (EDT)

Added support for ISOROPIA II

- The ISORROPIA II package performs aerosol thermodynamical equilibrium. It partitions nitrate (HNO3 and NIT) and ammonia (NH3 and NH4) between the gas and aerosol phases. Inputs to the partitioning routine include temperature and RH. ISORROPIA II has significant benefits over previous implementations of ISORROPIA, especially for partitioning of nitrate at low RH. Click here more information.

See Benchmarks results gcadj_std_v34i test 003 to 005

--Yanko 12:19, 22 April 2013 (EDT)

Added support for reaction rate constants defined in input.gcadj

- Reaction rate constants can now be selected as control variables for sensitivity analysis or optimization. The complete set of reaction rate constants, or subsets, can be specified in input.gcadj.

See Benchmarks results gcadj_std_v34m test 001 to 011

--Yanko 17:38, 25 June 2013 (EDT)


- Bug fixes in adjoint model

M Undefined

M Undefined on line 1199 of tagged_co_adj_mod.f, this only affects tagged_co emissions inversions.

--Yanko 19:06, 14 November 2012 (EST)

Error compiling on ifort 12

Fixed an error that made imposible to compile sciabr_co_obs_mod.f on ifort 12. The error was caused by an openmp pragma. This error is entirely a problem of the compiler and not the code itself, this should me resolved on version 13 of the compiler. Meanwhile we just commented the pragma to avoid problems.

--Yanko 19:06, 14 November 2012 (EST)

Set observation errors to 1% in pseudo-obs test

Setting the observation errors to 1% instead of 100% in the pseudo-obs test.

See Benchmarks results gcadj_std_v34a

--Yanko 14:08, 18 December 2012 (EST)

Fixed Makefile Bug

Fixed a Makefile bug preventing 'make help' from running at checkout, also added example of IFORT_OPT flag on run script.

--Yanko 15:53, 25 January 2013 (EST)

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