GEOS-Chem Adjoint v33: Difference between revisions

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== Overview ==
== Overview ==
PUBLIC RELEASE
Pipeline for future updates.
*Previous version: [[GEOS-Chem_Adjoint_v31]]
*Next version: [[GEOS-Chem_Adjoint_v33]]
== What's new in this version ==


=== Updates to forward model ===
*Previous version: [[GEOS-Chem_Adjoint_v32]]


=== Bug fixes in forward model ===


==== Ionic strength below zero in rpmares (adj33_001) ====
== Issues to resolve in the next release ==
On prospero, we often get the message: <tt>Ionic strength below zero...negative concentrations</tt>.
 
Despite the setting of negative roots to zero, sometimes the code still ends up with negative CRUTES.  Trap for it here to prevent mysterious crashing later.  Also, add the following
 
          !IF ( CRUTES(1) .ne. ABS(CRUTES(1) ) ) CRUTES(1)=1d9
          !IF ( CRUTES(2) .ne. ABS(CRUTES(2) ) ) CRUTES(2)=1d9
          !IF ( CRUTES(3) .ne. ABS(CRUTES(3) ) ) CRUTES(3)=1d9
 
which for some reason (I have no idea why) prevents the code from returning a negative CRUTES on prospero.
 
--[[User:Daven|Daven]] 14:58, 6 January 2012 (EST)
 
==== Updated lightning parameterization and fix for cloud-top-height algorithm (v9-01-01) ====
Updates to <tt>a6_read_mod.f</tt> and <tt>lightning_nox_mod.f</tt>.  Details in Lee's description: http://people.seas.harvard.edu/~ltmurray/LNOx.v9-01-01.Release.Notes.pd
 
--[[User:Daven|Daven]] 15:18, 6 January 2012 (EST)
 
==== Fix for GEIA emissions scaling factor over Botswana (v9-01-02h) ====
Updates to <tt>scale_anthro_mod.f</tt>.  See [[GEOS-Chem_v9-01-02#Fix_for_GEIA_emissions_scaling_factor_over_Botswana]]
 
--[[User:Daven|Daven]] 16:16, 6 January 2012 (EST)
 
==== TINY parameter in convection_mod.f (v8-03-02) ====
Update to <tt>convection_mod.f</tt> [[GEOS-Chem_v8-03-02#TINY_parameter_in_convection_mod.f]]
 
--[[User:Daven|Daven]] 16:16, 6 January 2012 (EST)
 
==== Updated to REGRID_05x0666_NESTED for non-standard domains (v?-?-?) ====
 
:I revised the SUBROUTINE REGRID_05x0666_NESTED.
 
:The problem in the original code is that the Longitude of LL (Left-Low of nested window) has to be even number and the latitude of LL  has to be integer number. It has no influence on our standard NA/CH/EU nested setting.
     
:I think it would be safer to fix this problem because we perhaps need to define new nested window in future.
 
This subroutine has now been replaced with Zhe's update. Not sure if there is a corresponding update in the v9 forward model yet.
 
--[[User:Daven|Daven]] 19:06, 6 January 2012 (EST)
 
=== Updates to adjoint model ===
 
=== Bug fixes in adjoint model ===
 
==== Mover error checking for O3 assimilation (adj33_002) ====
'''''[mailto:N.Bousserez@dal.ca Nicolas Bousserez] wrote:'''''
 
:the code crashes in "input_adj_mod.f" when doing the checking of observation settings (see line 2027 in my code). It is apparently due to "IDCSPEC_ADJ", which is not allocated/defined yet at the time the program executes those lines. I'm skipping these checks for now then. Note: The code crashes also when using "TES_O3_OBS" instead of "SCIA_DAL_NO2_OBS", so it is not related to what I implemented apparently.
 
The following block of code has been moved from <tt>input_adj_mod.f</tt> to subroutine <tt>INIT_CSPEC_ADJ</tt> in <tt>adj_arrays_mod.f</tt>, as it can only be called after the <tt>CSPEC</tt> variables have been initialized.
 
#elif defined ( TES_O3_OBS )
      ! Since the O3 obs operators will pass adjoints back
      ! to CSPEC via CSPEC_AFTER_CHEM_ADJ, we need to make sure that
      ! these species are listed as observed species
      FOUND = .FALSE.
      DO N = 1, NOBS_CSPEC
        IF ( TRIM( NAMEGAS( IDCSPEC_ADJ(N) ) ) == 'O3' ) THEN
            FOUND = .TRUE.
        ENDIF
      ENDDO
      IF ( .not. FOUND ) THEN
        CALL ERROR_STOP( ' Need to list O3 as observed species',
    &                    ' input_adj_mod ' )
      ENDIF
#endif
 
--[[User:Daven|Daven]] 16:38, 6 January 2012 (EST)
 
==== Retire CSPEC_NO2_ADJ (adj33_003) ====
 
'''''[mailto:N.Bousserez@dal.ca Nicolas Bousserez] wrote:'''''
 
:In "chemdr_adj.F" I removed this part:
#if defined( SCIA_KNMI_NO2_OBS ) || defined( SCIA_DAL_NO2_OBS )
! Apply forcing from satellite observations
CSPEC_ADJ(:,IDNO2) = CSPEC_ADJ(:,IDNO2) + CSPEC_NO2_ADJ(:)
CSPEC_NO2_ADJ(:) = 0d0
#endif
:because it seems like I'm already updating the adjoint of NO2 in "sciadal_no2_obs_mod.f" through CSPEC_AFTER_CHEM_ADJ. I would like to be sure that it is correct though.
 
'''''[mailto:daven.henze@colorado.edu Daven Henze] wrote:'''''
 
:Yes, that is correct.  I didn't want to take it out incase you had built your obs operator using CSPEC_NO2_ADJ.  But since you used the more generic CSPEC_AFTER_CHEM_ADJ, then we can delete this section entirely and use the section higher up in this file ( IF (LCSPEC_OBS) ...) to apply the forcing from your obs operator to CSPEC_ADJ.
 
Now use <tt>CSPEC_AFTER_CHEM_ADJ</tt> instead of <tt>CSPEC_NO2_ADJ</tt> in <tt>chemdr_adj.f</tt>.
 
--[[User:Daven|Daven]] 18:04, 6 January 2012 (EST)
 
==== Fix to NaNs in STT_ADJ everywhere after adjoint of partitioning (adj33_004) ====
The forward gas-phase chemical solver may sometimes need to repeat the internal integration of the reaction rate ODEs within a single grid cell.  When this happens, we now only redo the model calculation during the forward model run, not the adjoint, as this can lead to a corrupt CSPEC_ADJ array globally (not sure how that happens, but it does), eventually triggering a check for NaNs after the partitioning adjoint.  See updates to <tt>chemistry_mod.f</tt> and <tt>gckpp_adj_Integrator.f90</tt>.  Thanks to Richard Xu for helping pinpoint this bug.
 
--[[User:Daven|Daven]] 18:03, 6 January 2012 (EST)
 
==== Fix to NaNs in sulfate aerosol adjoint tracers (adj33_005) ====
Owing to cancelation of errors, it's possible to seemingly randomly end up with NaNs coming out of <tt>CHEM_SO2_ADJ</tt> .  This can happen if L3 ends up equaling 1d0 exactly.  We now trap for this and skip in the rate event this happens. 
 
--[[User:Daven|Daven]] 18:03, 6 January 2012 (EST)
 
==== Remove superfluous debugging which had <tt>LAVHRRLAI</tt> set to FALSE ====
Noted by Fabien.  Upated in <tt>input_mod.f</tt>.
 
--[[User:Daven|Daven]] 18:07, 6 January 2012 (EST)
 
==== Fix for reseting deposition adjoints (adj33_006) ====
 
'''''[mailto:fabienpaulot@gmail.com Fabien Paulot] wrote:'''''
 
:It seems it's "a bug" in the code. To keep track of the dry deposition flux of HNO3 I use dryhno3 (in cspec array). The CSPEC_ADJ(DRYHNO3,:) should be reset to zero at every time step but it is not. That's because you are saving in chk_cspec before it is reset to zero. Easy fix, just force to zero in chemdr_adj before the forcing is applied et voila, it works (the adjoint does not diverge any more after one hour). It should not affect anything as long as there is no forcing on dryhno3 (or any dry dep counters for that matter).
 
We add the following to reset the dry dep adjoints in <tt>chemdr_adj.f</tt>:
!$OMP PARALLEL DO
!$OMP+DEFAULT( SHARED )
!$OMP+PRIVATE( N, NK, JJ )
      DO N = 1,NUMDEP
          NK = NTDEP(N)
          IF (NK.NE.0) THEN
            JJ = IRM(NPRODLO+1,NK,NCS)
            IF (JJ.GT.0) THEN
                CSPEC_ADJ(:,JJ) = 0.0D0
            ENDIF
          ENDIF
      ENDDO
!$OMP END PARALLEL DO
 
--[[User:Daven|Daven]] 18:34, 6 January 2012 (EST)
 
==== Update comments for STT_ADJ unit conversion ====
'''''[mailto:mkeller@atmosp.physics.utoronto.ca Martin Keller] wrote:'''''
 
:I'm currently guessing that CONVERT_UNITS(1,etc.) does something like:
 
STT:    kg -> v/v
STT_ADJ: J/[v/v] -> J/kg
 
:and similarly CONVERT_UNITS(2,etc.)
 
STT:    v/v -> kg
STT_ADJ: J/kg -> J/[v/v]
 
:From a dimensional analysis this would seem plausible. It would also explain some of the errors I'm currently fighting with. If this is correct, then a short comment should perhaps be added to the code.
 
The comments in <tt>geos_chem_adj_mod.f</tt> have been updated surrounding calls to CONVERT_UNITS.
 
--[[User:Daven|Daven]] 18:43, 6 January 2012 (EST)
 
==== Only write upbd checkpoint files if necessary (adj33_007) ====
Thanks to Farhan Akhtar for pointing this out.  We now check to make sure writing these checkpoint files is necessary (i.e., it is an adjoint run, and not just a pseudo obs calculation) in <tt>linoz_mod.f</tt>:
 
      ! Now see if checkpointing is necessary (fa, dkh, 01/06/12, adj33_007)
      IF ( LADJ .and. N_CALC > 0 ) THEN
          CALL MAKE_UPBDFLX_CHKFILE( NYMD, NHMS, TAU )
      ENDIF
 
--[[User:Daven|Daven]] 18:54, 6 January 2012 (EST)
 
== Previous issues now resolved in v33 ==
 
== Previous issues now resolved in v32 ==
==== CO2 emissions update to allow for both monthly and years emissions ====
Update to <tt>co2_mod.f</tt>  (dkh, 03/07/11)
 
==== Updates to <tt>lidort_mod.f</tt> ====
*Reinstate NCOUNT in CALC_RF_FORCE so that aod files are made at the right time.  (dkh, 03/27/11)
*now check to make sure that MAXTHREADS matches JJPAR in lidort_mod.f (dkh, 03/27/11)
 
==== Update to Mie table ====
Update <tt>mie_mod.f</tt> to use finite difference values for adjoints. (dkh, 03/27/11)
 
==== Remove bug in <tt>SET_SF</tt> ====
Remove erroneous debugging code in <tt>subroutine SET_SF</tt> in <tt>inverse_mod.f</tt>. (dkh, 03/27/11)
 
 
== Outstanding issues not yet resolved in v33 ==

Revision as of 00:42, 7 January 2012

Overview

Pipeline for future updates.


Issues to resolve in the next release

Retrieved from "https://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_Adjoint_v33&oldid=9045"