GitHub Issue NOAA-EMC/GSI#337. Add capability to assimilate PM2.5 and VIIRS AOD for RRFS-CMAQ. #365

hongli-wang · 2022-04-20T20:22:15Z

Add capability to assimilate PM2.5 and VIIRS AOD for RRFS-CMAQ.

MichaelLueken · 2022-04-21T09:42:34Z

Hi @hongli-wang, there are three commit messages associated with this work. It should only be one. To reduce the number of commit messages from three to one, please use the following commands in your fork's feature/RRFS-CMAQ branch:

git reset --soft HEAD~1
git reset --soft HEAD~1
git commit --amend
Please save and close the commit message window without altering the current commit message.
git push origin feature/RRFS-CMAQ --force

The git reset --soft HEAD~1 command will remove the commit message, but retain the changes made for the commit. The git commit --amend command will commit the modified files to the current commit. Once the steps are complete, you will need to push the cleaned up branch back to the repository with the addition of the --force option.

I will go ahead and close PR #334 at this time.

If you have any questions, please let me know.

hongli-wang · 2022-04-21T14:09:23Z

Hi @hongli-wang, there are three commit messages associated with this work. It should only be one. To reduce the number of commit messages from three to one, please use the following commands in your fork's feature/RRFS-CMAQ branch:

git reset --soft HEAD~1

git reset --soft HEAD~1

git commit --amend

Please save and close the commit message window without altering the current commit message.

git push origin feature/RRFS-CMAQ --force

The git reset --soft HEAD~1 command will remove the commit message, but retain the changes made for the commit. The git commit --amend command will commit the modified files to the current commit. Once the steps are complete, you will need to push the cleaned up branch back to the repository with the addition of the --force option.

I will go ahead and close PR #334 at this time.

If you have any questions, please let me know.

@MichaelLueken-NOAA Thanks. I had followed the steps and pushed back to feature/RRFS-CMAQ.

MichaelLueken · 2022-04-21T14:17:18Z

@hongli-wang Thanks, the commit message looks good.

TingLei-NOAA · 2022-04-21T14:34:05Z

src/gsi/gsi_rfv3io_mod.f90

@@ -749,14 +759,98 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
    real(r_kind),dimension(:,:,:),pointer::ges_qg=>NULL()
    real(r_kind),dimension(:,:,:),pointer::ges_qnr=>NULL()
    real(r_kind),dimension(:,:,:),pointer::ges_w=>NULL()
+
+
+    real(r_kind),dimension(:,:,:),pointer::ges_aalj=>NULL()


This block of chem. Var declaration could be put into a include file? Using include files still conforms to GSI coding standard? @MichaelLueken-NOAA

Hi @TingLei-NOAA. What @hongli-wang has done here should be fine. There are no coding standards requiring the use of include files for blocks of variable declarations. Most of the GSI doesn't use include files. So, it would probably be best to leave the block of chem variable declarations as they currently are.

@MichaelLueken-NOAA , accepted. Thanks.
Then @hongli-wang , you can skip this comment.

Thank you all.

CoryMartin-NOAA

A few comments/questions, but mostly looks good I think. A lot of the if statements should be indented properly for readability.

CoryMartin-NOAA · 2022-04-21T14:13:45Z

src/gsi/amassaeromod.f90

+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it),'amassj',ges_amassj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it),'amassk',ges_amassk,istatus );ier=ier+istatus
+
+    if (ier/=0) then


Redundant extra if statement

agree. will fix. thanks.

CoryMartin-NOAA · 2022-04-21T14:14:27Z

src/gsi/amassaeromod.f90

+         do i=1,lat2
+            sv_rank3(i,j,k)=cv_amassj(i,j,k)*ges_aero(i,j,k)/ges_amassj(i,j,k)
+         if(ges_aero(i,j,k)/ges_amassj(i,j,k).ge.1.0)then
+           !print*,"amas2aero_tl:wg.ge.1 ",trim(aerosols(ic)),ges_aero(i,j,k),ges_amassj(i,j,k)


This if doesn't do anything if this is commented out.

This if doesn't do anything if this is commented out.

Agree. Deleted the if statement.

CoryMartin-NOAA · 2022-04-21T14:15:52Z

src/gsi/amassaeromod.f90

+   call gsi_bundlegetpointer (rval,trim(aerosols(ic)),sv_rank3,istatus);ier=ier+istatus
+   if (ier/=0) cycle
+
+   print*,"amass2aero_ad: sum= ",ic,trim(aerosols(ic)),sum(sv_rank3),sum(cv_amassi),sum(cv_amassj),sum(cv_amassk)


Isn't this going to print a lot of stuff to stdout (2 lines per processor per aerosol species)? Consider removing/commenting out.

commented out. Thanks.

CoryMartin-NOAA · 2022-04-21T14:22:54Z

src/gsi/chemmod.f90

@@ -164,8 +439,14 @@ function obs2model_anowbufr_pm()
       obs2model_anowbufr_pm=cmaq_pm
    elseif (wrf_mass_regional) then
       obs2model_anowbufr_pm=wrf_chem_pm
+!    elseif (fv3_cmaq_regional) then


is this intended to be commented out?

is this intended to be commented out?

yes. removed.

CoryMartin-NOAA · 2022-04-21T14:25:54Z

src/gsi/control2state.f90

      id=getindex(cvars3d,gases(ic))
      if (id>0) then
          call gsi_bundlegetpointer (sval(jj),gases(ic),sv_rank3,istatus)
          call gsi_bundlegetvar     (wbundle, gases(ic),sv_rank3,istatus)
+      !else


Can we remove this section if it is commented out?

Agree. Deleted.

CoryMartin-NOAA · 2022-04-21T14:34:18Z

src/gsi/obsmod.F90

@@ -157,6 +157,9 @@ module obsmod
 !                          GSI namelist level.  
 !  2020-09-15  Wu        - add option tcp_posmatch to mitigate possibility of erroneous TC initialization
 !  2020-09-19  CAPS(J. Park) - add 'vad_near_analtime' flag to assimilate newvad obs around analysis time only
+!   2021-11-16 Zhao      - add option l_obsprvdiag (if true) to trigger the output of


Same as before, why are these changes included here?

copied from emc master (Apr 5) which is a little advanced than mine ( March 8). Just realized this today.

CoryMartin-NOAA · 2022-04-21T14:34:49Z

src/gsi/read_aerosol.f90

+
+  ! new viirs table
+  character (len=69) :: vaodgstr1 = &
+      'SAID CLATH CLONH YEAR MNTH DAYS HOUR MINU SOZA SOLAZI RSST AOTQ RETRQ'


Does this break the global AOD regression test?

Never mind, I see the below boolean

CoryMartin-NOAA · 2022-04-21T14:35:56Z

src/gsi/read_aerosol.f90

              rsat = hdrvaodg(1); ksatid=rsat

-              if ( jsatid == 'NPP' .or. jsatid == 'npp' ) kidsat = 225
+              !if ( jsatid == 'NPP' .or. jsatid == 'npp' ) kidsat = 225


Remove this if it is the wrong code

The correct sat id for NPP should be 224.

CoryMartin-NOAA · 2022-04-21T14:36:34Z

src/gsi/read_guess.F90

@@ -171,6 +173,9 @@ subroutine read_guess(iyear,month,idd,mype)
        else if (fv3_regional      ) then
           call bg_fv3regfilenameg%init
           call  read_fv3_netcdf_guess(bg_fv3regfilenameg)
+           !if (fv3_cmaq_regional)then


Is this not needed because it will read it in the above line?

Previously I had a separated subroutine to read in the aero variables. But now, I keep this capability in the read_fv3_netcdf_guess. There is not such a subroutine anymore. I will remove the lines.

CoryMartin-NOAA · 2022-04-21T14:37:58Z

src/gsi/write_all.F90

@@ -121,6 +122,9 @@ subroutine write_all(increment)
  if (regional) then
     if (fv3_regional) then
        call wrfv3_netcdf(bg_fv3regfilenameg)
+        !if (fv3_cmaq_regional) then


Same question as in the read, if this isn't needed, remove, don't comment out.

will remove.

TingLei-NOAA · 2022-04-21T14:38:19Z

src/gsi/gsi_rfv3io_mod.f90

@@ -1018,6 +1180,109 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
         call GSI_BundleGetPointer ( GSI_MetGuess_Bundle(it), 'w' , ges_w ,istatus );ier=ier+istatus
      end if

+    if (laeroana_fv3cmaq) then


This block ( line1183-1284, laroana_fv3cmaq=.true.) and other similar blocks containing almost 100 lines can be put into one internal subroutine, and, hence, keep the main subroutine much cleaner

Thanks. will consider.

@hongli-wang I notice this kind of blocks containing about 100 lines of calls for GSI_BundleGetPointer sill exist. Would it be much more readable as suggested using a nested contain for a subroutine? To do this change only need a few vi actions . For this part, I made an example (successfully complied) in /scratch2/NCEPDEV/fv3-cam/Ting.Lei/dr-hongli/dr-pr-cmaq/GSI/src/gsi/gsi_rfv3io_mod.f90. A snipping shot is as

Searching "example" . Maybe, a better way is to create a module outside of gsi_rfv3io_mod.f90 to declare and do this kind of actions for this large patch of airosal variables. But current way is the least effort needed.

TingLei-NOAA · 2022-04-21T14:41:32Z

src/gsi/gsi_rfv3io_mod.f90

      endif

-      if( fv3sar_bg_opt == 0) then 
-        call GSI_BundleGetPointer ( gsibundle_fv3lam_dynvar_nouv, 'delp'  ,ges_delp ,istatus );ier=ier+istatus
+    if (laeroana_fv3cmaq) then


The same suggestions , this block when laeroana_fv3camq=.true.), could be put into a internal subroutine.
after that, this block would be like
^^
if (laeroana_fv3cmq) then
call aeroana_getpoint
endif
VV
That will look cleaner.

Thanks. will consider.

TingLei-NOAA · 2022-04-21T15:20:01Z

src/gsi/gsi_rfv3io_mod.f90

+        vartem=trim(name_chemvars3d(i))
+           if (ifindstrloc(aeronames_cmaq_fv3,trim(vartem)) > 0) then
+             jtracer=jtracer+1
+             fv3lam_io_tracerchemvars3d_nouv(jtracer)=trim(vartem)


A question: the chem. vars are also in the tracer file. If the IO of chem vars are delt along with other tracer files,
namely, combining fv3lam_io_tracerchemvars3d_nouv ( and corressponding IO bundle ) and fv3lam_io_tracervars3d_nouv,this will cause a more efficient/scalable parallel IO.
Will this add any significant complicities to the coding?

This is a good question/suggestion. I thought about this when I updated my code. If you think the combination will improve the efficiency of parallel IO, I may reconsider it. Thanks.

The current parallelization is done over number of variable number multiplied by the number of vertical levels. Assume, vertical levels are 60 levels, in the original tracers, there are two tracer variables , and , 7 chem. variables. In the current scheme, first, 2X60 fields would be distributed to various MPI processes and their IO (and conversion between native and analysis grids) would be done in parallel; second, after the first step, the similar would be done chem. variable, now, it is 7X60 fields would be deal with in parallel. If they are done together, there would be only one step: (2+7)X60 fields would be dealt with in parallel. In this case, if the number of mpi process is more than 120, then, in the first step of the current scheme, some MPI process would do nothing and namely the scalibility is not so well. Hope my explanation will help!

MichaelLueken · 2022-05-19T14:52:38Z

@CoryMartin-NOAA @TingLei-NOAA At your earliest convenience, please review that the modifications made by @hongli-wang address your concerns. If you are okay with the changes, please approve the PR. Otherwise, please note the issues that you have so that @hongli-wang may address them. Thank you very much for your time.

CoryMartin-NOAA · 2022-05-19T14:53:29Z

I will review by COB tomorrow.

TingLei-NOAA · 2022-05-19T20:03:17Z

Hi, Mike, I am starting to review it. But maybe, I will finish my reviewing till next week. Regards, Ting

…

______________________________ Ting Lei IMSG at NOAA/NWS/NCEP/EMC 5830 University Research Ct., Cubicle 2765 College Park, MD 20740 ***@***.*** 301-683-3624

On Thu, May 19, 2022 at 10:53 AM Cory Martin ***@***.***> wrote: I will review by COB tomorrow. — Reply to this email directly, view it on GitHub <#365 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APEFS7EC7VBPHOKYG7PLWK3VKZIXVANCNFSM5T5FCZ2A> . You are receiving this because you were mentioned.Message ID: ***@***.***>

TingLei-daprediction

Thanks to the developer for taking care of all the questions/suggestions.
This PR contains quite a lot of development in GSI, which have been implemented in GSI's style, which is not only efficient but also make the new codes have a good readability in terms of the coding itself.

CoryMartin-NOAA

Echoing Ting's comments, thanks for all of your hard work on this!

MichaelLueken · 2022-06-02T17:12:16Z

Hi @hongli-wang - Last Friday, I force-pushed an update to NOAA-EMC/GSI's develop branch. When I did this, your PR was force updated as well (since the branch associated with this PR was created directly from the develop branch). This has led to several conflicts and 10, rather than 1, commit message. To correct this:

git clone --recursive git@github.com:hongli-wang/GSI.git update
cd update
git checkout feature/RRFS-CMAQ
git submodule update
rm -rf libsrc/
git reset --soft HEAD~1
git reset --soft HEAD~1
git reset --soft HEAD~1
git reset --soft HEAD~1
git reset --soft HEAD~1
git reset --soft HEAD~1
git stash
git remote add upstream https://github.com/NOAA-EMC/GSI.git
git remote update
git rebase upstream/develop
git stash pop
vi jobs/JGDAS_ATMOS_ANALYSIS_DIAG

Remove lines 88, 91, 92, 93, and 94
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
- Remove export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
- Remove >>>>>>> Stashed changes

git add jobs/JGDAS_ATMOS_ANALYSIS_DIAG
vi jobs/JGDAS_ATMOS_CHGRES_FORENKF

Remove lines 90, 93, 94, 95, and 96
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
- Remove export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
- Remove >>>>>>> Stashed changes

git add jobs/JGDAS_ATMOS_CHGRES_FORENKF
vi jobs/JGDAS_ENKF_DIAG

Remove lines 85, 88, 89, 90, and 91
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
- Remove export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
- Remove >>>>>>> Stashed changes

git add jobs/JGDAS_ENKF_DIAG
vi jobs/JGDAS_ENKF_ECEN

Remove lines 93, 96, 97, 98, and 99
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
- Remove export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
- Remove >>>>>>> Stashed changes

git add jobs/JGDAS_ENKF_ECEN
vi jobs/JGDAS_ENKF_SELECT_OBS

Remove lines 85, 88, 89, 90, and 91
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
- Remove export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
- Remove >>>>>>> Stashed changes

git add jobs/JGDAS_ENKF_SELECT_OBS
vi jobs/JGDAS_ENKF_SFC

Remove lines 93, 96, 97, 98, and 99
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
- Remove export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
- Remove >>>>>>> Stashed changes

git add jobs/JGDAS_ENKF_SFC
vi jobs/JGLOBAL_ATMOS_ANALYSIS

Remove lines 88, 91, 92, 93, and 94
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
- Remove export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
- Remove >>>>>>> Stashed changes

git add jobs/JGLOBAL_ATMOS_ANALYSIS
vi jobs/JGLOBAL_ATMOS_ANALYSIS_CALC

Remove lines 88, 91, 92, 93, and 94
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
- Remove export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
- Remove >>>>>>> Stashed changes

git add jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
vi modulefiles/gsi_cheyenne.gnu.lua

Remove lines 12, 14, 15, 16, 22, 26, 27, 33, 35, 36, and 37
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove prepend_path("MODULEPATH", "/glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.2.0/modulefiles/stack")
- Remove >>>>>>> Stashed changes
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove >>>>>>> Stashed changes
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove pushenv("MKLROOT", "/glade/u/apps/opt/intel/2021.2/mkl/latest")
- Remove >>>>>>> Stashed changes

git add modulefiles/gsi_cheyenne.gnu.lua
vi modulefiles/gsi_cheyenne.intel.lua

Remove lines 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, and 29
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove load("intel/2021.2")
- Remove load("mpt/2.22")
- Remove load("ncarcompilers/0.5.0")
- Remove prepend_path("MODULEPATH", "/glade/p/ral/jntp/GMTB/tools/hpc-stack-v1.2.0/modulefiles/stack")
- Remove load("hpc/1.2.0")
- Remove load("hpc-intel/2021.2")
- Remove load("hpc-mpt/2.22")
- Remove load("mkl/2021.2")
- Remove >>>>>>> Stashed changes

git add modulefiles/gsi_cheyenne.intel.lua
vi src/GSD/gsdcloud/CMakeLists.txt

Remove lines 25, 29, 30, 31, 32, and 33
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -convert big_endian")
- Remove elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
- Remove set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fconvert=big-endian")
- Remove >>>>>>> Stashed changes

git add src/GSD/gsdcloud/CMakeLists.txt
vi src/gsi/gsi_files.cmake

Remove lines 81, 82, and 84
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove >>>>>>> Stashed changes

git add src/gsi/gsi_files.cmake
vi src/gsi/gsi_rfv3io_mod.f90

Remove lines 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, and 113
- Remove <<<<<<< Updated upstream
- Remove character(len=max_varname_length), dimension(ndynvarslist), parameter :: &
- Remove vardynvars = [character(len=max_varname_length) :: &
- Remove "u","v","u_w","u_s","v_w","v_s","t","tv","tsen","w","delp","ps","delzinc"]
- Remove character(len=max_varname_length), dimension(ntracerslist), parameter :: &
- Remove vartracers = [character(len=max_varname_length) :: &
- Remove 'q','oz','ql','qi','qr','qs','qg','qnr']
- Remove character(len=max_varname_length), dimension(15), parameter :: &
- Remove varfv3name = [character(len=max_varname_length) :: &
- Remove 'u','v','W','T','delp','sphum','o3mr','liq_wat','ice_wat','rainwat','snowwat','graupel','rain_nc','ps','DZ'], &
- Remove vgsiname = [character(len=max_varname_length) :: &
- Remove 'u','v','w','tsen','delp','q','oz','ql','qi','qr','qs','qg','qnr','ps','delzinc']
- Remove =======
- Remove >>>>>>> Stashed changes

git add src/gsi/gsi_rfv3io_mod.f90
vi src/ncdiag/cmake/ncdiag_compiler_flags_Intel_Fortran.cmake

Remove lines 5, 7, 8, and 9
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -assume byterecl -convert big_endian -implicitnone")
- Remove >>>>>>> Stashed changes

git add src/ncdiag/cmake/ncdiag_compiler_flags_Intel_Fortran.cmake
vi util/cmake/gsiutils_compiler_flags_Intel_Fortran.cmake

Remove lines 5, 7, 8, and 9
- Remove <<<<<<< Updated upstream
- Remove =======
- Remove set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS} -g -traceback -implicitnone")
- Remove >>>>>>> Stashed changes

git add util/cmake/gsiutils_compiler_flags_Intel_Fortran.cmake
git submodule update
git reset HEAD util/Radiance_Monitor/image_gen/html/sum_thumbs.tar
git commit -m "GitHub Issue NOAA-EMC/GSI#337. Add capability to assimilate PM2.5 and VIIRS AOD in RRFS-CMAQ."
git push origin feature/RRFS-CMAQ --force

This should correct the conflicts and bring the number of commit messages back to 1. If you have any questions or encounter any issues, please let me know.

hongli-wang · 2022-06-02T17:40:19Z

@MichaelLueken-NOAA I will take care the conflicts evening. Since most of files are unrelated to my changes, I may check out gsi develop branch and copy the files there to resolve the conflicts. I will let you know when I resolve the conflicts. Thanks!

hongli-wang · 2022-06-06T17:39:31Z

@MichaelLueken-NOAA I will take care the conflicts evening. Since most of files are unrelated to my changes, I may check out gsi develop branch and copy the files there to resolve the conflicts. I will let you know when I resolve the conflicts. Thanks!

@MichaelLueken-NOAA I have pushed the changes back by fellowing your instructions. Please double check and let me know if you see any issues. Thanks again!

MichaelLueken

I have completed my initial review of your changes. Please ensure that all if statements and do loops have at least two-space indentation. Please ensure that all real and integer declarations need either a length (i_kind) or precision (r_kind) and all real values need a precision (_r_kind). Please ensure that modified lines don't exceed the 132 character limit. Please ensure that all .ge., .lt., and .eq. are replaced with >=, <, and ==, respectively. Please ensure that implicit none is included for all subroutines.

I haven't run the regression tests yet. I also haven't tried compiling the changes using GNU compilers. I'll return with any issues that might show while attempting to run the regression (standard and debug) tests and compiling with GNU.

MichaelLueken · 2022-07-05T10:32:44Z

src/gsi/amassaeromod.f90

+
+
+! Get background amassi,amassj,amassk 
+   ier = 0.0


ier is an integer. Please use 0 rather than real 0.0

MichaelLueken · 2022-07-05T10:37:04Z

src/gsi/amassaeromod.f90

+  real(r_kind),pointer,dimension(:,:,:) :: ges_amassk=>NULL()
+
+
+    ier = 0.0


ier is an integer. Please replace 0.0 with 0.

MichaelLueken · 2022-07-05T10:37:32Z

src/gsi/amassaeromod.f90

+
+! ad of partitioning amass into aerosol speccies 
+  do ic=1,naerosols
+   ier = 0.0


ier is an integer. Please replace 0.0 with 0.

MichaelLueken · 2022-07-05T10:41:39Z

src/gsi/amassaeromod.f90

+do ic=1,naerosols
+   call GSI_BundleGetPointer (GSI_ChemGuess_Bundle(it),trim(aerosols(ic)),ges_aero,istatus )
+   call gsi_bundlegetpointer (sval,trim(aerosols(ic)),sv_rank3,istatus)
+   if (istatus/=0) cycle
+   sv_rank3=zero
+   if(imodes_cmaq_fv3(ic).eq.1)then
+   do k=1,nsig
+      do j=1,lon2
+         do i=1,lat2
+            sv_rank3(i,j,k)=cv_amassi(i,j,k)*ges_aero(i,j,k)/ges_amassi(i,j,k)
+         end do
+      end do
+   end do
+   elseif(imodes_cmaq_fv3(ic).eq.2)then
+   do k=1,nsig
+      do j=1,lon2
+         do i=1,lat2
+            sv_rank3(i,j,k)=cv_amassj(i,j,k)*ges_aero(i,j,k)/ges_amassj(i,j,k)
+         end do
+      end do
+   end do
+   else
+   do k=1,nsig
+      do j=1,lon2
+         do i=1,lat2
+            sv_rank3(i,j,k)=cv_amassk(i,j,k)*ges_aero(i,j,k)/ges_amassk(i,j,k)
+         end do
+      end do
+   end do
+
+   end if
+end do
+
+return


Please align line 78 with line 75. Please ensure all if statements and do loops have at least two-space indentation. Please replace .eq. with == on lines 83 and 91.

MichaelLueken · 2022-07-05T10:42:49Z

src/gsi/amassaeromod.f90

+  do ic=1,naerosols
+   ier = 0.0
+   call GSI_BundleGetPointer (GSI_ChemGuess_Bundle(it),trim(aerosols(ic)),ges_aero,istatus );ier=ier+istatus
+   call gsi_bundlegetpointer (rval,trim(aerosols(ic)),sv_rank3,istatus);ier=ier+istatus
+   if (ier/=0) cycle
+
+   if(imodes_cmaq_fv3(ic).eq.1)then
+   do k=1,nsig
+      do j=1,lon2
+         do i=1,lat2
+            cv_amassi(i,j,k)=cv_amassi(i,j,k)+sv_rank3(i,j,k)*ges_aero(i,j,k)/ges_amassi(i,j,k)
+         end do
+      end do
+   end do
+   elseif(imodes_cmaq_fv3(ic).eq.2)then
+   do k=1,nsig
+      do j=1,lon2
+         do i=1,lat2
+            cv_amassj(i,j,k)=cv_amassj(i,j,k)+sv_rank3(i,j,k)*ges_aero(i,j,k)/ges_amassj(i,j,k)
+         end do
+      end do
+   end do
+   else
+   do k=1,nsig
+      do j=1,lon2
+         do i=1,lat2
+            cv_amassk(i,j,k)=cv_amassk(i,j,k)+sv_rank3(i,j,k)*ges_aero(i,j,k)/ges_amassk(i,j,k)
+         end do
+      end do
+   end do
+
+   end if
+  end do


Please align line 154 with line 151. Please ensure all if statements and do loops have at least two-space indentation. Please replace .eq. with == on lines 160 and 168.

MichaelLueken · 2022-07-06T13:29:46Z

src/gsi/gsi_rfv3io_mod.f90

+!    real(r_kind),dimension(:,:,:),pointer::ges_pm25at=>NULL()
+!    real(r_kind),dimension(:,:,:),pointer::ges_pm25ac=>NULL()
+!    real(r_kind),dimension(:,:,:),pointer::ges_pm25co=>NULL()
+!    real(r_kind),dimension(:,:,:),pointer::ges_pm2_5=>NULL()
+
+!    real(r_kind),dimension(:,:,:),pointer::ges_amassi=>NULL()
+!    real(r_kind),dimension(:,:,:),pointer::ges_amassj=>NULL()
+!    real(r_kind),dimension(:,:,:),pointer::ges_amassk=>NULL()


Please remove commented out lines if you won't be using them in the future.

MichaelLueken · 2022-07-06T13:30:24Z

src/gsi/gsi_rfv3io_mod.f90

+    if (laeroana_fv3cmaq)then
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aalj',ges_aalj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'acaj',ges_acaj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'acli',ges_acli,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aclj',ges_aclj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aclk',ges_aclk,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'acors',ges_acors,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aeci',ges_aeci,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aecj',ges_aecj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'afej',ges_afej,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aivpo1j',ges_aivpo1j,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'akj',ges_akj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'alvoo1i',ges_alvoo1i,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'alvoo2i',ges_alvoo2i,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'alvpo1i',ges_alvpo1i,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'alvpo1j',ges_alvpo1j,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'amgj',ges_amgj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'amnj',ges_amnj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'anai',ges_anai,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'anaj',ges_anaj,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'anh4i',ges_anh4i,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'anh4j',ges_anh4j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'anh4k',ges_anh4k,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'ano3i',ges_ano3i,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'ano3j',ges_ano3j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'ano3k',ges_ano3k,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aothri',ges_aothri,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aothrj',ges_aothrj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aseacat',ges_aseacat,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asij',ges_asij,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aso4i',ges_aso4i,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aso4j',ges_aso4j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aso4k',ges_aso4k,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asoil',ges_asoil,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvoo1i',ges_asvoo1i,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvoo2i',ges_asvoo2i,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvpo1i',ges_asvpo1i,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvpo1j',ges_asvpo1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvpo2i',ges_asvpo2i,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvpo2j',ges_asvpo2j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvpo3j',ges_asvpo3j,istatus );ier=ier+istatus
+
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'atij',ges_atij,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'atol1j',ges_atol1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'atol2j',ges_atol2j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'atol3j',ges_atol3j,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'abnz1j',ges_abnz1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'abnz2j',ges_abnz2j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'abnz3j',ges_abnz3j,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aiso1j',ges_aiso1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aiso2j',ges_aiso2j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aiso3j',ges_aiso3j,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'atrp1j',ges_atrp1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'atrp2j',ges_atrp2j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asqtj' ,ges_asqtj,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aalk1j',ges_aalk1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aalk2j',ges_aalk2j,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'apah1j',ges_apah1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'apah2j',ges_apah2j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'apah3j',ges_apah3j,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aorgcj',ges_aorgcj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aolgbj',ges_aolgbj,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'aolgaj',ges_aolgaj,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'alvoo1j',ges_alvoo1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'alvoo2j',ges_alvoo2j,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvoo1j',ges_asvoo1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvoo2j',ges_asvoo2j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'asvoo3j',ges_asvoo3j,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'apcsoj',ges_apcsoj,istatus );ier=ier+istatus
+
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'axyl1j',ges_axyl1j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'axyl2j',ges_axyl2j,istatus );ier=ier+istatus
+    call GSI_BundleGetPointer ( GSI_ChemGuess_Bundle(it), 'axyl3j',ges_axyl3j,istatus );ier=ier+istatus
+    end if


Please ensure at least two-space indentation for all if statements.

MichaelLueken · 2022-07-06T13:30:47Z

src/gsi/gsi_rfv3io_mod.f90

+    if (laeroana_fv3cmaq) then
+    call gsi_copy_bundle(GSI_ChemGuess_Bundle(it),gsibundle_fv3lam_tracerchem_nouv)
+    end if


Please ensure at least two-space indentation for all if statements.

MichaelLueken · 2022-07-06T13:31:27Z

src/gsi/gsi_rfv3io_mod.f90

+      if (laeroana_fv3cmaq) then
+      call gsi_fv3ncdf_write(grd_fv3lam_tracerchem_ionouv,gsibundle_fv3lam_tracerchem_nouv, &
+                             add_saved,fv3filenamegin%tracers,fv3filenamegin)
+      endif


Please ensure at least two-space indentation for if statements.

MichaelLueken · 2022-07-06T13:31:52Z

src/gsi/gsi_rfv3io_mod.f90

+      if (laeroana_fv3cmaq) then
+      call gsi_fv3ncdf_write_v1(grd_fv3lam_tracerchem_ionouv,gsibundle_fv3lam_tracerchem_nouv,&
+                                add_saved,fv3filenamegin%tracers,fv3filenamegin)
+      endif


Please ensure at least two-space indentation for if statements.

MichaelLueken

Thank you very much for making updates following my review, @hongli-wang! There are a few more issues to iron out, then this work should be ready for the review committee.

MichaelLueken · 2022-07-12T13:22:04Z

src/gsi/crtm_interface.f90

@@ -555,10 +559,16 @@ subroutine init_crtm(init_pass,mype_diaghdr,mype,nchanl,nreal,isis,obstype,radmo
 if (radmod%laerosol_fwd) then 
    if(.not.allocated(aero)) allocate(aero(nsig,n_actual_aerosols))
    if(.not.allocated(aero_conc)) allocate(aero_conc(msig,n_actual_aerosols),auxrh(msig))
+!wang    if(.not.allocated(aero_wc)) allocate(aero_wc(msig,n_actual_aerosols)) 


Please remove name from comment. If code won't be used in the future, please remove the line.

MichaelLueken · 2022-07-12T13:31:10Z

src/gsi/set_crtm_aerosolmod.f90

+             aerosol(i)%type  = SULFATE_CMAQ_AEROSOL 
+           case ('aclj','aclk','anai','anaj','aseacat')
+             aerosol(i)%type  = SEASALT_AEROSOL
+           case ('aivpo1j','alvpo1i','alvpo1j','aothri','aothrj','asvpo1i','asvpo1j','asvpo2i','asvpo2j','asvpo3j','atol1j','axyl1j','axyl2j','axyl3j')


This line exceeds the 132 character limit. Please break this line down so that it doesn't exceed 132 characters.

Please break up this line that exceeds the 132 character limit.

MichaelLueken · 2022-07-12T13:33:17Z

src/gsi/setupaod.f90

@@ -373,13 +373,36 @@ subroutine setupaod(obsLL,odiagLL,lunin,mype,nchanl,nreal,nobs,&
                 case( 23 )     ! over bright land surface, high quality
                    tnoise = 0.0550472_r_kind+ 0.299558_r_kind*aod_obs
               end select
+               if (fv3_cmaq_regional)then
+                  if (aod_obs(n_viirs_550nm) .lt. 0.4_r_kind)then


Please replace .lt. with <

MichaelLueken · 2022-07-12T13:34:16Z

src/gsi/setupaod.f90

+        if (obstype == 'viirs_aod' .and. fv3_cmaq_regional)then
+           do i = 1, nchanl
+             if ( i /= n_viirs_550nm) cycle
+             if (aod_obs(i) .lt. 0.4_r_kind) then


Please replace .lt. with <

MichaelLueken · 2022-07-12T13:34:34Z

src/gsi/setupaod.f90

+             if (aod_obs(i) .lt. 0.4_r_kind) then
+                aod_obs(i) = aod_obs(i) - ( 0.41_r_kind*aod_obs(i)-0.03_r_kind )
+             end if
+             if (aod_obs(i) .ge. 0.4_r_kind .and. aod_obs(i) .lt. 0.9_r_kind)then


Please replace .ge. with >= and .lt. with <

src/gsi/gsi_rfv3io_mod.f90

MichaelLueken · 2022-07-12T13:53:23Z

src/gsi/gsi_rfv3io_mod.f90

@@ -1566,7 +2001,12 @@ subroutine gsi_fv3ncdf_read(grd_ionouv,cstate_nouv,filenamein,fv3filenamegin)
    endif
    do ilevtot=kbgn,kend
      vgsiname=grd_ionouv%names(1,ilevtot)
+      ! write(6,*)' gsi_fv3ncdf_read_wang1: ',ilevtot,vgsiname


Please remove debug write statement.

MichaelLueken · 2022-07-12T13:53:42Z

src/gsi/gsi_rfv3io_mod.f90

@@ -1591,8 +2031,10 @@ subroutine gsi_fv3ncdf_read(grd_ionouv,cstate_nouv,filenamein,fv3filenamegin)
          deallocate(uu2d_layout)
        enddo
      else
+       !write(6,*)' gsi_fv3ncdf_read_wang2: ',ilevtot,varname


Please remove debug write.

MichaelLueken · 2022-07-12T13:53:54Z

src/gsi/gsi_rfv3io_mod.f90

        iret=nf90_inq_varid(gfile_loc,trim(adjustl(varname)),var_id)
        iret=nf90_get_var(gfile_loc,var_id,uu2d,start=startloc,count=countloc)
+       !write(6,*)' gsi_fv3ncdf_read_wang3: ',ilevtot,var_id,sum(uu2d)


Please remove debug write.

MichaelLueken

Hi @hongli-wang. The code compiles using Intel and GNU compilers without issues. The regression tests were run and all passed successfully. While compiling in debug, there were several unused variables in your changes that will need to be addressed (either removed or commented out) and have been noted in the review. Also, there was a subscript warning that will need to be addressed (the location and warning message are in this latest review). With respect to alignment in gsi_rfv3io_mod.f90 and stppm2_5, the if statements and do loops need to begin in the same column as the preceding line, then ensure two-space indentation within the if statements and do loops. In set_crtm_aerosolmod, please ensure that the line that exceeds 132 characters is broken up (line 131) and that all real values have a precision (_r_kind) associated with them.

src/gsi/set_crtm_aerosolmod.f90

MichaelLueken · 2022-07-14T09:35:37Z

src/gsi/set_crtm_aerosolmod.f90

+             aerosol(i)%type  = SULFATE_CMAQ_AEROSOL 
+           case ('aclj','aclk','anai','anaj','aseacat')
+             aerosol(i)%type  = SEASALT_AEROSOL
+           case ('aivpo1j','alvpo1i','alvpo1j','aothri','aothrj','asvpo1i','asvpo1j','asvpo2i','asvpo2j','asvpo3j','atol1j','axyl1j','axyl2j','axyl3j')


Please break up this line that exceeds the 132 character limit.

src/gsi/stppm2_5.f90

src/gsi/setuppm2_5.f90

src/gsi/stppm2_5.f90

src/gsi/amassaeromod.f90

src/gsi/crtm_interface.f90

src/gsi/read_aerosol.f90

MichaelLueken

Thank you very much, @hongli-wang! There is one more indentation issue in src/gsi_rfv3io_mod.90 that needs to be addressed, then I should be able to submit this work to the review committee.

MichaelLueken · 2022-07-18T10:09:43Z

src/gsi/gsi_rfv3io_mod.f90

@@ -953,6 +1070,35 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
          write(6,*)'fv3lam_io_dynmetvars2d_nouv is ',(trim(fv3lam_io_dynmetvars2d_nouv(i)),i=1,ntracerio3d)
      endif      

+    if (laeroana_fv3cmaq) then


Please indent line 1073 by two spaces to align with line 1071 above.

MichaelLueken · 2022-07-18T10:10:53Z

src/gsi/gsi_rfv3io_mod.f90

@@ -953,6 +1070,35 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
          write(6,*)'fv3lam_io_dynmetvars2d_nouv is ',(trim(fv3lam_io_dynmetvars2d_nouv(i)),i=1,ntracerio3d)
      endif      

+    if (laeroana_fv3cmaq) then
+      jtracer = 0


Please indent line 1074 by two spaces for proper if statement indentation.

MichaelLueken · 2022-07-18T10:14:58Z

src/gsi/gsi_rfv3io_mod.f90

+    if (laeroana_fv3cmaq) then
+      jtracer = 0
+!name_chemvars3d chemguess from anavinfo
+      do i=1,size(name_chemvars3d)


Please indent line 1076 by two spaces for proper if statement indentation.

MichaelLueken · 2022-07-18T10:15:38Z

src/gsi/gsi_rfv3io_mod.f90

+      jtracer = 0
+!name_chemvars3d chemguess from anavinfo
+      do i=1,size(name_chemvars3d)
+        vartem=trim(name_chemvars3d(i))


Please indent line 1077 by two spaces for proper do loop indentation.

MichaelLueken · 2022-07-18T10:16:20Z

src/gsi/gsi_rfv3io_mod.f90

+!name_chemvars3d chemguess from anavinfo
+      do i=1,size(name_chemvars3d)
+        vartem=trim(name_chemvars3d(i))
+        if (ifindstrloc(aeronames_cmaq_fv3,trim(vartem)) > 0) then


Please indent line 1078 by two spaces for proper do loop indentation.

MichaelLueken · 2022-07-18T10:34:56Z

src/gsi/gsi_rfv3io_mod.f90

+      fv3lam_io_tracerchemvars3d_nouv(jtracer+3)="pm25co"
+      fv3lam_io_tracerchemvars3d_nouv(jtracer+4)="pm2_5"
+      fv3lam_io_tracerchemvars3d_nouv(jtracer+5)="amassi"
+      fv3lam_io_tracerchemvars3d_nouv(jtracer+6)="amassj"


Please indent line 1093 by two spaces for proper if statement indentation.

MichaelLueken · 2022-07-18T10:35:13Z

src/gsi/gsi_rfv3io_mod.f90

+      fv3lam_io_tracerchemvars3d_nouv(jtracer+4)="pm2_5"
+      fv3lam_io_tracerchemvars3d_nouv(jtracer+5)="amassi"
+      fv3lam_io_tracerchemvars3d_nouv(jtracer+6)="amassj"
+      fv3lam_io_tracerchemvars3d_nouv(jtracer+7)="amassk"


Please indent line 1074 by two spaces for proper if statement indentation.

MichaelLueken · 2022-07-18T10:35:41Z

src/gsi/gsi_rfv3io_mod.f90

+      fv3lam_io_tracerchemvars3d_nouv(jtracer+6)="amassj"
+      fv3lam_io_tracerchemvars3d_nouv(jtracer+7)="amassk"
+
+      if (mype == 0) then


Please indent line 1096 by two spaces for proper if statement indentation.

MichaelLueken · 2022-07-18T10:36:01Z

src/gsi/gsi_rfv3io_mod.f90

+      fv3lam_io_tracerchemvars3d_nouv(jtracer+7)="amassk"
+
+      if (mype == 0) then
+        write(6,*) ' fv3lam_io_tracerchemvars3d_nouv is',(trim(fv3lam_io_tracerchemvars3d_nouv(i)),i=1,ntracerchemio3d)


Please indent line 1097 by two spaces for proper if statement indentation.

MichaelLueken · 2022-07-18T10:36:38Z

src/gsi/gsi_rfv3io_mod.f90

+
+      if (mype == 0) then
+        write(6,*) ' fv3lam_io_tracerchemvars3d_nouv is',(trim(fv3lam_io_tracerchemvars3d_nouv(i)),i=1,ntracerchemio3d)
+      endif


Please indent line 1098 by two spaces for proper if statement indentation.

MichaelLueken

Thanks for addressing my concerns, @hongli-wang. Once the current work has been merged to the authoritative repository tomorrow, I will submit this work to the review committee.

hongli-wang · 2022-07-19T13:31:19Z

Thanks for addressing my concerns, @hongli-wang. Once the current work has been merged to the authoritative repository tomorrow, I will submit this work to the review committee.

@MichaelLueken-NOAA Thank for your comments and let me know if you have other concerns.

MichaelLueken · 2022-07-20T18:00:00Z

Hi @hongli-wang. An update to src/gsi/gsi_rfv3io_mod has been merged to the authoritative repository that causes a conflict with your update. Please rebase the authoritative develop branch to your feature/RRFS-CMAQ branch, then I should be able to submit your work to the review committee.

…RS AOD in RRFS-CMAQ.

hongli-wang · 2022-07-20T18:41:08Z

Hi @MichaelLueken-NOAA, I just rebased my code, it seems no conflict now.

MichaelLueken · 2022-07-28T16:46:19Z

The due date for feedback from the review committee has past with no feedback, so I will now give final approval to these changes and merge this work to the authoritative develop branch.

MichaelLueken requested review from TingLei-NOAA, CoryMartin-NOAA, MichaelLueken, hu5970 and dtkleist April 21, 2022 09:28

MichaelLueken linked an issue Apr 21, 2022 that may be closed by this pull request

Add capability to assimilate PM2.5 and VIIRS AOD in RRFS-CMAQ #337

Closed

MichaelLueken mentioned this pull request Apr 21, 2022

Commit PM2.5 and AOD DA development for RRFS-CMAQ #334

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hongli-wang force-pushed the feature/RRFS-CMAQ branch from 12f5982 to 8bbfc17 Compare April 21, 2022 14:04

TingLei-NOAA reviewed Apr 21, 2022

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CoryMartin-NOAA reviewed Apr 21, 2022

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TingLei-NOAA reviewed Apr 21, 2022

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hongli-wang force-pushed the feature/RRFS-CMAQ branch from 8bbfc17 to ae51201 Compare May 4, 2022 19:08

lgannoaa mentioned this pull request May 10, 2022

v16.3 DA pre-implementation parallel NOAA-EMC/global-workflow#776

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hongli-wang force-pushed the feature/RRFS-CMAQ branch 9 times, most recently from cbed89b to 840cb19 Compare May 19, 2022 14:18

hongli-wang force-pushed the feature/RRFS-CMAQ branch from c54a8c4 to 0afecd7 Compare May 25, 2022 21:46

TingLei-daprediction approved these changes May 25, 2022

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CoryMartin-NOAA approved these changes May 27, 2022

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MichaelLueken force-pushed the develop branch from 1cadb36 to 047b5da Compare May 27, 2022 16:21

hongli-wang force-pushed the feature/RRFS-CMAQ branch from 0afecd7 to dbd3f2c Compare June 6, 2022 17:36

hongli-wang force-pushed the feature/RRFS-CMAQ branch from dbd3f2c to 466ad51 Compare June 7, 2022 19:12

MichaelLueken suggested changes Jul 6, 2022

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hongli-wang force-pushed the feature/RRFS-CMAQ branch 3 times, most recently from 60e29a1 to bbd4721 Compare July 11, 2022 21:16

MichaelLueken suggested changes Jul 12, 2022

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hongli-wang force-pushed the feature/RRFS-CMAQ branch from bbd4721 to 86bfa71 Compare July 13, 2022 18:50

MichaelLueken suggested changes Jul 14, 2022

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hongli-wang force-pushed the feature/RRFS-CMAQ branch 2 times, most recently from 0637009 to f936ad3 Compare July 15, 2022 20:12

MichaelLueken suggested changes Jul 19, 2022

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hongli-wang force-pushed the feature/RRFS-CMAQ branch from f936ad3 to 54520ac Compare July 19, 2022 13:24

MichaelLueken approved these changes Jul 19, 2022

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hongli-wang force-pushed the feature/RRFS-CMAQ branch from 54520ac to 3f5374a Compare July 20, 2022 18:22

GitHub Issue NOAA-EMC#337. Add capability to assimilate PM2.5 and VII…

38f938f

…RS AOD in RRFS-CMAQ.

hongli-wang force-pushed the feature/RRFS-CMAQ branch from 3f5374a to 38f938f Compare July 20, 2022 18:39

MichaelLueken changed the title ~~Feature/rrfs cmaq~~ GitHub Issue NOAA-EMC/GSI#337. Add capability to assimilate PM2.5 and VIIRS AOD for RRFS-CMAQ. Jul 28, 2022

MichaelLueken merged commit 863da47 into NOAA-EMC:develop Jul 28, 2022

		real(r_kind),pointer,dimension(:,:,:) :: ges_amassk=>NULL()


		ier = 0.0

GitHub Issue NOAA-EMC/GSI#337. Add capability to assimilate PM2.5 and VIIRS AOD for RRFS-CMAQ. #365

GitHub Issue NOAA-EMC/GSI#337. Add capability to assimilate PM2.5 and VIIRS AOD for RRFS-CMAQ. #365

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TingLei-NOAA Apr 21, 2022 • edited Loading

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TingLei-NOAA Apr 21, 2022 •

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