Merge pull request #416 from GEOS-ESM/feature/sdrabenh/GEOS-FP-5_44_into_main

Author: mathomp4

CHANGELOG.md

@@ -13,12 +13,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
-- Fix for Open MPI calls in `esma_mpirun` from Open MPI 5 testing
-
 ### Removed
 
 ### Deprecated
 
+## [2.1.7] - 2026-04-15
+
+### Added
+
+- Minor changes for VIIRS additions
+
+### Changed
+
+- Synced latest changes from branch GEOS-FP-5_44 into main
+
+### Fixed
+
+- Fix for Open MPI calls in `esma_mpirun` from Open MPI 5 testing
+
 ## [2.1.6] - 2026-01-06
 
 ### Fixed
@@ -85,6 +97,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+2026-01-17:
+
+- added GOES, HIMAWARI, VIIRS SNPP & NOAA-20, and Lunar AERONET aerosol observations to the KX-lists
+
+2026-01-12:
+
+- r_dist for MILAN
+- minor bug fix in ODS code
+- add ak/bk for MLT 1st version
+- add ability to write out akbk to nc4 (JEDI support)
+
+------------
 - fix vED
 - SLES15 stuff
 - fix to reading of table in time ave program

GMAO_etc/r_dist

@@ -401,8 +401,8 @@ return $put_rc;
 sub resolve {
 
     my ( $LOCALROOT,$REMOTEROOT,$expno,$yyyy,$yy,$mm,$dd,$hh,$file ) = @_;
-    $file =~ s/\${REMOTEROOT}/$REMOTEROOT/g;
-    $file =~ s/\${LOCALROOT}/$LOCALROOT/g;
+    $file =~ s/\$\{REMOTEROOT}/$REMOTEROOT/g;
+    $file =~ s/\$\{LOCALROOT}/$LOCALROOT/g;
     $file =~ s/%y4/$yyyy/g;
     $file =~ s/%y2/$yy/g;
     $file =~ s/%m2/$mm/g;

GMAO_etc/setup_gaas_obs.pl

@@ -15,7 +15,7 @@ if ( NOT HERMES_LIGHT )
      m_insitu.F m_interp.F90 m_lp.F m_maph.F90 m_maph_pert.F90 m_mapz.F m_mapz_pert.F90
      m_qsat.F m_remap.f90 m_set_eta.F90 m_vdc2vdc.F90 progsig.f90 shared_topo_remap.F90 m_topo_remap.F90
      m_interpack.F m_interpack_ad.F m_ec_set_eta.F90 m_ecdyn.f90 m_tick.f90
-     m_dyn_util.F90 m_spline.f90 m_nc_JEDIinc.f90
+     m_dyn_util.F90 m_spline.f90 m_nc_JEDIinc.f90 m_nc_akbk.f90
      )
 
    esma_add_library(${this} SRCS ${srcs} DEPENDENCIES GMAO_mpeu GMAO_gfio_r8)

GMAO_hermes/CMakeLists.txt

@@ -14,6 +14,7 @@ program dyn2dyn
       use m_dyn
       use m_set_eta, only : set_ncep72,unset_ncep72
       use m_dyn2dyn, only : dyn2dyn_do
+      use m_topo_remap, only: dyn_topo_remap
 
       use m_StrTemplate        ! grads style templates
 
@@ -75,6 +76,7 @@ program dyn2dyn
 !     ------
       character(len=255) msg
       character(len=255), pointer :: xtrnames(:)
+      character(len=255) phfile
       integer, parameter :: READ_ONLY = 1
       integer fid, nvars, ngatts
       integer ier, ifile
@@ -97,7 +99,7 @@ program dyn2dyn
                                 fakedate, nymdf, nhmsf, &
                                 dophys, expid, RCfile, verbose, oldana, force, &
                                 vectype, dgrid, ncep72, ncf, pncf, indxlevs, &
-                                xtrnames )
+                                xtrnames, phfile )
 
 
 !  Loop over input eta files
@@ -155,6 +157,12 @@ program dyn2dyn
          end if
          if(ncep72) call set_ncep72
 
+!        If topographic remap requested ...
+!        ----------------------------------
+         if ( trim(phfile) /= "NONE" ) then
+            call dyn_topo_remap(trim(phfile), w_e, vectype, ier)
+         endif
+ 
 !        Perform interpolation
 !        ---------------------
          if ( trim(RCfile)=='NONE' ) then
@@ -211,7 +219,7 @@ subroutine Init_ ( mfiles, etafiles, nfiles, dynfile, lwifile, &
                          fakedate, nymdf, nhmsf,                     &
                          dophys, expid, RCfile, verbose, oldana, force, &
                          vectype, dgrid, ncep72, ncf, pncf, indxlevs, &
-                         xtrnames )
+                         xtrnames, phfile )
 
       implicit NONE
 
@@ -245,6 +253,7 @@ subroutine Init_ ( mfiles, etafiles, nfiles, dynfile, lwifile, &
       logical,       intent(out) :: pncf    ! non-complaint dyn-perturbation file knob
       logical,       intent(out) :: indxlevs! index levels (in place of pressure levs)
       character(len=*), pointer  :: xtrnames(:)
+      character(len=*) :: phfile
 
 !
 ! !REVISION HISTORY:
@@ -319,6 +328,7 @@ subroutine Init_ ( mfiles, etafiles, nfiles, dynfile, lwifile, &
       trnames = 'NONE'
       im_usr = -1
       jm_usr = -1
+      phfile = 'NONE'
 
 !     Parse command line
 !     ------------------
@@ -466,6 +476,10 @@ subroutine Init_ ( mfiles, etafiles, nfiles, dynfile, lwifile, &
                ncf = .true.
            case ('-pncf')
                pncf = .true.
+           case ("-phfile")
+             if ( iarg+1 .gt. argc ) call usage()
+             iarg = iarg + 1
+             call GetArg ( iarg, phfile )
            case ('-prec')
             if ( iarg+1 .gt. argc ) call usage()
             iarg = iarg + 1
@@ -604,6 +618,7 @@ subroutine usage()
       print *, '-ncf          non-compliant dyn-vector (see NOTES)'
       print *, '-pncf         non-compliant dyn-vector perturbation (see NOTES)'
       print *, '-tracers N,M  read/write extra tracers of name N and M from ori file to new'
+      print *, '-phfile FNAME when alternative dyn-vec file provided, will perform topo-remap'
       print *
       print *, ' NOTES:'
       print *, '   1)  For the time being, in order to do horizontal'

GMAO_hermes/dyn2dyn.f90

@@ -2,6 +2,7 @@ program eta_echo
 use m_set_eta, only: set_eta
 use m_set_eta, only: get_ref_plevs
 use m_spline, only: spline
+use m_nc_akbk, only: write_nc_akbk
 implicit none
 
 integer :: nlevs,mlevs
@@ -13,6 +14,7 @@ program eta_echo
 real(4) :: ak4,bk4
 real(4) :: pbottom
 character(len=255) :: locfname
+character(len=255) :: akbkfname
 
 call init_
 
@@ -28,7 +30,7 @@ program eta_echo
     call write_plevs_()
 endif
 
-call write_akbk_()
+if ( akbkfname /= "NULL" ) call write_nc_akbk ( akbkfname, ak8, bk8 )
 
 deallocate(ak8,bk8)
 
@@ -52,13 +54,15 @@ subroutine init_
      print *, " -mlevs LEVS - interpolate to this level setting"
      print *, " -plevs      - echoes pressure levels"
      print *, " -r4         - single precision"
+     print *, " -nc FILE    - writes out ak/bk to nc4 file"
      print *, "   "
      stop
   end if
   bot2top = .false.
   lsingle = .false.
   lplevs = .false.
   locfname = "NULL"
+  akbkfname = "NULL"
   pbottom = -999.
   mlevs=0
   iarg = 1
@@ -84,6 +88,10 @@ subroutine init_
          iarg = iarg + 1
          call GetArg ( iarg, argv )
          locfname = trim(argv)
+     case ("-nc")
+         iarg = iarg + 1
+         call GetArg ( iarg, argv )
+         akbkfname = trim(argv)
      case default
         read(argv,*) nlevs
      end select

GMAO_hermes/eta_echo.f90

@@ -0,0 +1,94 @@
+module m_nc_akbk
+use netcdf
+implicit none
+private
+public :: write_nc_akbk
+interface write_nc_akbk
+  module procedure write_nc_akbk_
+end interface
+integer :: mype_ = 0 
+integer :: root_ = 0 
+contains
+subroutine write_nc_akbk_ (fname,ak, bk)
+
+  character(len=*), intent(in) :: fname
+  double precision, intent(in) :: ak(:), bk(:)
+
+  ! NetCDF variables
+  integer :: ncid, dimid_edge
+  integer :: varid_edge, varid_ak, varid_bk
+  integer :: rc
+  integer :: i, km
+  double precision, allocatable :: edge(:)
+  
+  km = size(ak)
+  allocate(edge(km))
+  do i=1,km
+    edge(i) = dble(i)
+  enddo
+ 
+  ! Create the NetCDF file
+  call check_( nf90_create(fname, NF90_CLOBBER, ncid), rc, mype_, root_ )
+  if(rc/=0) return
+
+  ! Define dimensions
+  call check_ ( nf90_def_dim(ncid, "edge", km, dimid_edge), rc, mype_, root_ )
+  if(rc/=0) return
+
+  ! Define variables
+  call check_ ( nf90_def_var(ncid, "edge", NF90_DOUBLE, (/dimid_edge/), varid_edge), rc, mype_, root_ )
+  call check_ ( nf90_def_var(ncid, "ak",   NF90_DOUBLE, (/dimid_edge/), varid_ak), rc, mype_, root_ )
+  call check_ ( nf90_def_var(ncid, "bk",   NF90_DOUBLE, (/dimid_edge/), varid_bk), rc, mype_, root_ )
+
+  ! Add attributes to edge
+  call check_ ( nf90_put_att(ncid, varid_edge, "units", "level"), rc, mype_, root_ )
+  call check_ ( nf90_put_att(ncid, varid_edge, "long_name", "sigma at layer edges"), rc, mype_, root_ )
+  call check_ ( nf90_put_att(ncid, varid_edge, "standard_name", "atmosphere_hybrid_sigma_pressure_coordinate"),&
+                             rc, mype_, root_ )
+  call check_ ( nf90_put_att(ncid, varid_edge, "coordinate", "eta"), rc, mype_, root_ )
+  call check_ ( nf90_put_att(ncid, varid_edge, "positive", "down"), rc, mype_, root_ )
+  call check_ ( nf90_put_att(ncid, varid_edge, "formulaTerms", "ap: ak b: bk ps: ps p0: p00"),&
+                             rc, mype_, root_ )
+
+  ! Add attributes to ak
+  call check_ ( nf90_put_att(ncid, varid_ak, "long_name", "hybrid_sigma_pressure_a"),&
+                rc, mype_, root_ )
+  call check_ ( nf90_put_att(ncid, varid_ak, "units", "Pa"), rc, mype_, root_ )
+
+  ! Add attributes to bk
+  call check_ ( nf90_put_att(ncid, varid_bk, "long_name", "hybrid_sigma_pressure_b"), &
+                rc, mype_, root_ )
+  call check_ ( nf90_put_att(ncid, varid_bk, "units", "1"), rc, mype_, root_ )
+
+  ! Global attributes
+  call check_ ( nf90_put_att(ncid, NF90_GLOBAL, "NASA/GMAO", &
+       "Homepage = http://gmao.gfsc.nasa.gov/"), rc, mype_, root_ )
+
+  ! End define mode
+  call check_ ( nf90_enddef(ncid), rc, mype_, root_ )
+
+  ! Write data
+  call check_ ( nf90_put_var(ncid, varid_edge, edge), rc, mype_, root_ )
+  call check_ ( nf90_put_var(ncid, varid_ak, ak), rc, mype_, root_ )
+  call check_ ( nf90_put_var(ncid, varid_bk, bk), rc, mype_, root_ )
+
+  ! Close file
+  call check_ ( nf90_close(ncid), rc, mype_, root_ )
+
+  deallocate(edge)
+
+  print *, "NetCDF file ",trim(fname)," written successfully."
+
+end subroutine write_nc_akbk_
+subroutine check_(status,rc, myid, root)
+    integer, intent ( in) :: status
+    integer, intent (out) :: rc
+    integer, intent ( in) :: myid, root
+    rc=0
+    if(status /= nf90_noerr) then
+      if(myid==root) print *, trim(nf90_strerror(status))
+      rc=999
+    end if
+end subroutine check_
+end module m_nc_akbk
+