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Modified oned/obs_diag.f90 to add an unused singleton level #791

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merged 3 commits into from
Jan 9, 2025
Merged

Modified oned/obs_diag.f90 to add an unused singleton level #791

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ebcfa9d
Modified oned/obs_diag.f90 to add an unused singleton level
jlaucar Jan 8, 2025
346ce9a
bump version and changelog for release
hkershaw-brown Jan 9, 2025
6cf8c4a
Merge branch 'main' into oned_obs_diag_fix
hkershaw-brown Jan 9, 2025
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7 changes: 7 additions & 0 deletions CHANGELOG.rst
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Expand Up @@ -22,6 +22,13 @@ individual files.

The changes are now listed with the most recent at the top.

**January 9 2024 :: Bug-fix 1D obs_diag. Tag v11.8.7**

- Added a dummy dimension so 1D obs_diag output can be used with
MATLAB diagnostic tools
- Added a notification that probit inflation QCEFF options are ignored
for RTPS

**December 6 2024 :: Developer tests. Tag v11.8.6**

- Tests for distribution modules: normal, beta, gamma
Expand Down
83 changes: 55 additions & 28 deletions assimilation_code/programs/obs_diag/oned/obs_diag.f90
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Expand Up @@ -68,6 +68,8 @@ program obs_diag
integer, parameter :: MaxRegions = 4
integer, parameter :: MaxTrusted = 5
integer, parameter :: stringlength = 32
! Output files need a single level to be compatible with three D fields for plotting
integer, parameter :: Nlevels = 1

!---------------------------------------------------------------------
! variables associated with the observation
Expand Down Expand Up @@ -1728,6 +1730,7 @@ subroutine WriteNetCDF(fname)
character(len=*), intent(in) :: fname

integer :: ncid, i, nobs, typesdimlen
integer :: LevelDimID, LevelVarID
integer :: RegionDimID, RegionVarID
integer :: TimeDimID, TimeVarID
integer :: CopyDimID, CopyVarID, CopyMetaVarID
Expand Down Expand Up @@ -1880,6 +1883,7 @@ subroutine WriteNetCDF(fname)
call nc_check(nf90_def_dim(ncid=ncid, &
name='time', len = NF90_UNLIMITED, dimid = TimeDimID), &
'WriteNetCDF', 'time:def_dim '//trim(fname))

call nc_check(nf90_def_dim(ncid=ncid, &
name='bounds', len = 2, dimid = BoundsDimID), &
'WriteNetCDF', 'bounds:def_dim '//trim(fname))
Expand All @@ -1892,6 +1896,10 @@ subroutine WriteNetCDF(fname)
name='obstypes', len = max_defined_types_of_obs, dimid = TypesDimID), &
'WriteNetCDF', 'types:def_dim '//trim(fname))

call nc_check(nf90_def_dim(ncid=ncid, &
name='level', len = 1, dimid = LevelDimID), &
'WriteNetCDF', 'level:def_dim '//trim(fname))

call nc_check(nf90_def_dim(ncid=ncid, &
name='region', len = Nregions, dimid = RegionDimID), &
'WriteNetCDF', 'region:def_dim '//trim(fname))
Expand Down Expand Up @@ -1926,6 +1934,22 @@ subroutine WriteNetCDF(fname)
call nc_check(nf90_put_att(ncid, TypesVarID, 'explanation', 'see ObservationTypes'), &
'WriteNetCDF', 'types:explanation')

!----------------------------------------------------------------------------
! Define 'level' dimension
!----------------------------------------------------------------------------

call nc_check(nf90_def_var(ncid=ncid, name='level', xtype=nf90_int, &
dimids=LevelDimID, varid=LevelVarID), 'WriteNetCDF', 'level:def_var')
call nc_check(nf90_put_att(ncid, LevelVarID, 'long_name', 'model level'), &
'WriteNetCDF', 'level:long_name')
call nc_check(nf90_put_att(ncid, LevelVarID, 'units', 'nondimensional'), &
'WriteNetCDF', 'level:units')
! Level values are -1 to reflect that they are not meaningful
call nc_check(nf90_put_att(ncid, LevelVarID, 'valid_range', (/-1, -1/)), &
'WriteNetCDF', 'level:valid_range')
call nc_check(nf90_put_att(ncid, LevelVarID, 'explanation', 'needed for compatibility with 3D'), &
'WriteNetCDF', 'level:explanation')

!----------------------------------------------------------------------------
! Define the regions coordinate variable and attributes
!----------------------------------------------------------------------------
Expand All @@ -1939,7 +1963,7 @@ subroutine WriteNetCDF(fname)
call nc_check(nf90_put_att(ncid, RegionVarID, 'valid_range', (/1,Nregions/)), &
'WriteNetCDF', 'region:valid_range')
call nc_check(nf90_put_att(ncid, RegionVarID, 'explanation', 'see region_names'), &
'WriteNetCDF', 'types:explanation')
'WriteNetCDF', 'region:explanation')

!----------------------------------------------------------------------------
! Define 'bounds' dimension
Expand Down Expand Up @@ -2055,6 +2079,9 @@ subroutine WriteNetCDF(fname)
call nc_check(nf90_put_var(ncid, TypesMetaVarID, obs_type_strings(1:max_defined_types_of_obs)), &
'WriteNetCDF', 'typesmeta:put_var')

call nc_check(nf90_put_var(ncid, LevelVarID, (/ -1 /)), &
'WriteNetCDF', 'level:put_var')

call nc_check(nf90_put_var(ncid, RegionVarID, (/ (i,i=1,Nregions) /) ), &
'WriteNetCDF', 'region:put_var')

Expand All @@ -2078,13 +2105,13 @@ subroutine WriteNetCDF(fname)

if ( verbose ) write(*,*)'summary for Priors of time-region vars'
if ( create_rank_histogram ) then
ierr = WriteTRV(ncid, prior, TimeDimID, CopyDimID, RegionDimID, RankDimID)
ierr = WriteTRV(ncid, prior, TimeDimID, CopyDimID, LevelDimID, RegionDimID, RankDimID)
else
ierr = WriteTRV(ncid, prior, TimeDimID, CopyDimID, RegionDimID)
ierr = WriteTRV(ncid, prior, TimeDimID, CopyDimID, LevelDimID, RegionDimID)
endif
if ( verbose ) write(*,*)
if ( verbose ) write(*,*)'summary for Posteriors of time-region vars'
ierr = WriteTRV(ncid, poste, TimeDimID, CopyDimID, RegionDimID)
ierr = WriteTRV(ncid, poste, TimeDimID, CopyDimID, LevelDimID, RegionDimID)
if ( verbose ) write(*,*)

!----------------------------------------------------------------------------
Expand All @@ -2100,10 +2127,10 @@ end subroutine WriteNetCDF
!======================================================================


function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, RegionDimID, RankDimID)
function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, LevelDimID, RegionDimID, RankDimID)
integer, intent(in) :: ncid
type(TRV_type), intent(in) :: vrbl
integer, intent(in) :: TimeDimID, CopyDimID, RegionDimID
integer, intent(in) :: TimeDimID, CopyDimID, RegionDimID, LevelDimID
integer, optional, intent(in) :: RankDimID
integer :: WriteTRV

Expand All @@ -2112,7 +2139,7 @@ function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, RegionDimID, RankDimID)
character(len=NF90_MAX_NAME) :: string1

integer :: VarID, VarID2, oldmode
real(r4), allocatable, dimension(:,:,:) :: rchunk
real(r4), allocatable, dimension(:,:,:, :) :: rchunk
integer, allocatable, dimension(:,:,:) :: ichunk

FLAVORS : do ivar = 1,num_obs_types
Expand All @@ -2124,31 +2151,31 @@ function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, RegionDimID, RankDimID)
write(*,'(i4,1x,A,1x,i8)') ivar, obs_type_strings(ivar), nobs
endif

allocate(rchunk(Nregions,Ncopies,Nepochs))
allocate(rchunk(Nregions,Nlevels, Ncopies, Nepochs))
rchunk = MISSING_R4

do itime = 1,Nepochs
do iregion = 1,Nregions

rchunk(iregion, 1,itime) = vrbl%Nposs( itime,iregion,ivar)
rchunk(iregion, 2,itime) = vrbl%Nused( itime,iregion,ivar)
rchunk(iregion, 3,itime) = vrbl%rmse( itime,iregion,ivar)
rchunk(iregion, 4,itime) = vrbl%bias( itime,iregion,ivar)
rchunk(iregion, 5,itime) = vrbl%spread( itime,iregion,ivar)
rchunk(iregion, 6,itime) = vrbl%totspread( itime,iregion,ivar)
rchunk(iregion, 7,itime) = vrbl%NbadDartQC( itime,iregion,ivar)
rchunk(iregion, 8,itime) = vrbl%observation(itime,iregion,ivar)
rchunk(iregion, 9,itime) = vrbl%ens_mean( itime,iregion,ivar)
rchunk(iregion,10,itime) = vrbl%Ntrusted( itime,iregion,ivar)
rchunk(iregion,11,itime) = vrbl%NDartQC_0( itime,iregion,ivar)
rchunk(iregion,12,itime) = vrbl%NDartQC_1( itime,iregion,ivar)
rchunk(iregion,13,itime) = vrbl%NDartQC_2( itime,iregion,ivar)
rchunk(iregion,14,itime) = vrbl%NDartQC_3( itime,iregion,ivar)
rchunk(iregion,15,itime) = vrbl%NDartQC_4( itime,iregion,ivar)
rchunk(iregion,16,itime) = vrbl%NDartQC_5( itime,iregion,ivar)
rchunk(iregion,17,itime) = vrbl%NDartQC_6( itime,iregion,ivar)
rchunk(iregion,18,itime) = vrbl%NDartQC_7( itime,iregion,ivar)
rchunk(iregion,19,itime) = vrbl%NDartQC_8( itime,iregion,ivar)
rchunk(iregion, 1, 1,itime) = vrbl%Nposs( itime,iregion,ivar)
rchunk(iregion, 1, 2,itime) = vrbl%Nused( itime,iregion,ivar)
rchunk(iregion, 1, 3,itime) = vrbl%rmse( itime,iregion,ivar)
rchunk(iregion, 1, 4,itime) = vrbl%bias( itime,iregion,ivar)
rchunk(iregion, 1, 5,itime) = vrbl%spread( itime,iregion,ivar)
rchunk(iregion, 1, 6,itime) = vrbl%totspread( itime,iregion,ivar)
rchunk(iregion, 1, 7,itime) = vrbl%NbadDartQC( itime,iregion,ivar)
rchunk(iregion, 1, 8,itime) = vrbl%observation(itime,iregion,ivar)
rchunk(iregion, 1, 9,itime) = vrbl%ens_mean( itime,iregion,ivar)
rchunk(iregion,1, 10,itime) = vrbl%Ntrusted( itime,iregion,ivar)
rchunk(iregion,1, 11,itime) = vrbl%NDartQC_0( itime,iregion,ivar)
rchunk(iregion,1, 12,itime) = vrbl%NDartQC_1( itime,iregion,ivar)
rchunk(iregion,1, 13,itime) = vrbl%NDartQC_2( itime,iregion,ivar)
rchunk(iregion,1, 14,itime) = vrbl%NDartQC_3( itime,iregion,ivar)
rchunk(iregion,1, 15,itime) = vrbl%NDartQC_4( itime,iregion,ivar)
rchunk(iregion,1, 16,itime) = vrbl%NDartQC_5( itime,iregion,ivar)
rchunk(iregion,1, 17,itime) = vrbl%NDartQC_6( itime,iregion,ivar)
rchunk(iregion,1, 18,itime) = vrbl%NDartQC_7( itime,iregion,ivar)
rchunk(iregion,1, 19,itime) = vrbl%NDartQC_8( itime,iregion,ivar)

enddo
enddo
Expand All @@ -2161,7 +2188,7 @@ function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, RegionDimID, RankDimID)
string1 = trim(obsname)//'_'//adjustl(vrbl%string)

call nc_check(nf90_def_var(ncid, name=string1, xtype=nf90_real, &
dimids=(/ RegionDimID, CopyDimID, TimeDimID /), &
dimids=(/ RegionDimID, LevelDimID, CopyDimID, TimeDimID /), &
varid=VarID), 'WriteTRV', 'region:def_var')
call nc_check(nf90_put_att(ncid, VarID, '_FillValue', MISSING_R4), &
'WriteTRV','put_att:fillvalue')
Expand Down
2 changes: 1 addition & 1 deletion conf.py
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Expand Up @@ -21,7 +21,7 @@
author = 'Data Assimilation Research Section'

# The full version, including alpha/beta/rc tags
release = '11.8.7'
release = '11.8.8'
root_doc = 'index'

# -- General configuration ---------------------------------------------------
Expand Down
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