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Adding code to analyze the siginificant wave heigh in GSI 3D Analysis (see issue #601) #614

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merged 12 commits into from
Sep 29, 2023
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Adding code to analyze the siginificant wave heigh in GSI 3D Analysis (see issue #601) #614

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e117611
Adding code to analyze the siginificant wave heigh in GSI 3D Analysis,
GangZhao-NOAA Aug 22, 2023
8fd2251
Merge branch 'develop' into feature/3drtma_howv
GangZhao-NOAA Sep 1, 2023
f603756
some modifications to the code of analysis of significant wave height
GangZhao-NOAA Sep 13, 2023
8020227
Merge remote-tracking branch 'upstream/develop' into feature/3drtma_howv
GangZhao-NOAA Sep 13, 2023
8432590
based on feedback from code reviewers, modified the code of analysis
GangZhao-NOAA Sep 14, 2023
f3db06b
Merge branch 'develop' into feature/3drtma_howv
GangZhao-NOAA Sep 14, 2023
67b02a9
Minor modification in src/gsi/gsi_rfv3io_mod.f90 for reading howv in
GangZhao-NOAA Sep 15, 2023
1a4bab4
Merge remote-tracking branch 'upstream/develop' into feature/3drtma_howv
GangZhao-NOAA Sep 21, 2023
aa08628
minor modifications for analysis of significant wave height based on
GangZhao-NOAA Sep 21, 2023
7888831
trivial modification (fixing a typo)
GangZhao-NOAA Sep 21, 2023
99dd00a
Merge remote-tracking branch 'upstream/develop' into feature/3drtma_howv
GangZhao-NOAA Sep 26, 2023
f6031bd
minor modifications based on the feedback from code reviewers on the
GangZhao-NOAA Sep 26, 2023
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73 changes: 69 additions & 4 deletions src/gsi/gsi_rfv3io_mod.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@ module gsi_rfv3io_mod
! used as background for surface observation operator
! 2022-04-15 Wang - add IO for regional FV3-CMAQ (RRFS-CMAQ) model
! 2022-08-10 Wang - add IO for regional FV3-SMOKE (RRFS-SMOKE) model
! 2023-07-30 Zhao - add IO for the analysis of the significant wave height
! (SWH, aka howv in GSI) in fv3-lam based DA (eg., RRFS-3DRTMA)
!
! subroutines included:
! sub gsi_rfv3io_get_grid_specs
Expand Down Expand Up @@ -56,6 +58,7 @@ module gsi_rfv3io_mod
use rapidrefresh_cldsurf_mod, only: i_use_2mq4b,i_use_2mt4b
use chemmod, only: naero_cmaq_fv3,aeronames_cmaq_fv3,imodes_cmaq_fv3,laeroana_fv3cmaq
use chemmod, only: naero_smoke_fv3,aeronames_smoke_fv3,laeroana_fv3smoke
use rapidrefresh_cldsurf_mod, only: i_howv_in_anav, i_howv_in_data

implicit none
public type_fv3regfilenameg
Expand Down Expand Up @@ -134,6 +137,7 @@ module gsi_rfv3io_mod
public :: mype_qi,mype_qr,mype_qs,mype_qg,mype_qnr,mype_w
public :: k_slmsk,k_tsea,k_vfrac,k_vtype,k_stype,k_zorl,k_smc,k_stc
public :: k_snwdph,k_f10m,mype_2d,n2d,k_orog,k_psfc,k_t2m,k_q2m
public :: k_howv ! index for the significant wave height (aka howv in GSI)
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public :: ijns,ijns2d,displss,displss2d,ijnz,displsz_g
public :: fv3lam_io_dynmetvars3d_nouv,fv3lam_io_tracermetvars3d_nouv
public :: fv3lam_io_tracerchemvars3d_nouv,fv3lam_io_tracersmokevars3d_nouv
Expand All @@ -145,6 +149,7 @@ module gsi_rfv3io_mod

integer(i_kind) k_slmsk,k_tsea,k_vfrac,k_vtype,k_stype,k_zorl,k_smc,k_stc
integer(i_kind) k_snwdph,k_f10m,mype_2d,n2d,k_orog,k_psfc,k_t2m,k_q2m
integer(i_kind) k_howv ! index for the significant wave height (aka howv in GSI)
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parameter( &
k_f10m =1, & !fact10
k_stype=2, & !soil_type
Expand All @@ -159,7 +164,10 @@ module gsi_rfv3io_mod
k_t2m =11, & ! 2 m T
k_q2m =12, & ! 2 m Q
k_orog =13, & !terrain
n2d=13 )
k_howv =14, & ! significant wave height (aka howv in GSI)
n2d=14 ) ! It might be better if n2d is a variable
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! depending on the variables in the list of
! anavinfo, instead of a constant parameter.
logical :: grid_reverse_flag
character(len=max_varname_length),allocatable,dimension(:) :: fv3lam_io_dynmetvars3d_nouv
! copy of cvars3d excluding uv 3-d fields
Expand Down Expand Up @@ -767,6 +775,8 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
! 2022-04-01 Y. Wang and X. Wang - add capability to read reflectivity
! for direct radar EnVar DA using reflectivity as state
! variable, poc: xuguang.wang@ou.edu
! 2023-07-30 Zhao - added code to read significant wave height (howv) field
! from the 2D fv3-lam firstguess file (fv3_sfcdata).
! attributes:
! language: f90
! machine: ibm RS/6000 SP
Expand Down Expand Up @@ -816,6 +826,7 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
real(r_kind),pointer,dimension(:,:,:):: ges_delp =>NULL()
real(r_kind),dimension(:,:),pointer::ges_t2m=>NULL()
real(r_kind),dimension(:,:),pointer::ges_q2m=>NULL()
real(r_kind),dimension(:,:),pointer::ges_howv=>NULL() ! --> howv

real(r_kind),dimension(:,:,:),pointer::ges_ql=>NULL()
real(r_kind),dimension(:,:,:),pointer::ges_qi=>NULL()
Expand Down Expand Up @@ -1093,6 +1104,7 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
if(mype == 0) write(6,*)'the metvarname ',trim(vartem),' will be dealt separately'
else if(trim(vartem)=='t2m') then
else if(trim(vartem)=='q2m') then
else if(trim(vartem)=='howv') then ! ??
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else
write(6,*)'the metvarname2 ',trim(vartem),' has not been considered yet, stop'
call stop2(333)
Expand All @@ -1110,7 +1122,8 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
do i=1,size(name_metvars2d)
vartem=trim(name_metvars2d(i))
if(.not.( (trim(vartem)=='ps'.and.fv3sar_bg_opt==0).or.(trim(vartem)=="z") &
.or.(trim(vartem)=="t2m").or.(trim(vartem)=="q2m"))) then !z is treated separately
.or.(trim(vartem)=="t2m").or.(trim(vartem)=="q2m") &
.or.(trim(vartem)=="howv"))) then ! z is treated separately
if (ifindstrloc(vardynvars,trim(vartem)) > 0) then
jdynvar=jdynvar+1
fv3lam_io_dynmetvars2d_nouv(jdynvar)=trim(vartem)
Expand Down Expand Up @@ -1365,6 +1378,13 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
call GSI_BundleGetPointer ( GSI_MetGuess_Bundle(it),'t2m',ges_t2m,istatus );ier=ier+istatus
if (ier/=0) call die(trim(myname),'cannot get pointers for t2m,ier=',ier)
endif

!--- significant wave height (howv)
if ( i_howv_in_anav == 1 ) then
call GSI_BundleGetPointer(GSI_MetGuess_Bundle(it),'howv',ges_howv,istatus ); ier=ier+istatus
if (ier/=0) call die(trim(myname),'cannot get pointers for howv, ier=',ier)
endif
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if(mype == 0 ) then
call check(nf90_open(fv3filenamegin(it)%dynvars,nf90_nowrite,loc_id))
call check(nf90_inquire(loc_id,formatNum=ncfmt))
Expand Down Expand Up @@ -1546,7 +1566,7 @@ subroutine read_fv3_netcdf_guess(fv3filenamegin)
endif


call gsi_fv3ncdf2d_read(fv3filenamegin(it),it,ges_z,ges_t2m,ges_q2m)
call gsi_fv3ncdf2d_read(fv3filenamegin(it),it,ges_z,ges_t2m,ges_q2m,ges_howv) ! adding code to read howv
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if(i_use_2mq4b > 0 .and. i_use_2mt4b > 0 ) then
! Convert 2m guess mixing ratio to specific humidity
Expand Down Expand Up @@ -1782,7 +1802,7 @@ end subroutine gsi_bundlegetpointer_fv3lam_tracerchem_nouv

end subroutine read_fv3_netcdf_guess

subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m)
subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m,ges_howv)
!$$$ subprogram documentation block
! . . . .
! subprogram: gsi_fv3ncdf2d_read
Expand All @@ -1792,6 +1812,8 @@ subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m)
! Scatter the field to each PE
! program history log:
! 2023-02-14 Hu - Bug fix for read in subdomain surface restart files
! 2023-07-30 Zhao - added IO to read significant wave height (howv) from 2D FV3-LAM
! firstguess file (fv3_sfcdata)
!
! input argument list:
! it - time index for 2d fields
Expand All @@ -1806,22 +1828,27 @@ subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m)
!$$$ end documentation block
use kinds, only: r_kind,i_kind
use mpimod, only: ierror,mpi_comm_world,npe,mpi_rtype,mype
use mpimod, only: mpi_itype ! used to broadcast an integer
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combine Line 1831 with Line 1830 and remove the comment

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Will do. Thank you!

use guess_grids, only: fact10,soil_type,veg_frac,veg_type,sfc_rough, &
sfct,sno,soil_temp,soil_moi,isli
use gridmod, only: lat2,lon2,itotsub,ijn_s
use general_commvars_mod, only: ltosi_s,ltosj_s
use netcdf, only: nf90_open,nf90_close,nf90_get_var,nf90_noerr
use netcdf, only: nf90_nowrite,nf90_inquire,nf90_inquire_dimension
use netcdf, only: nf90_inquire_variable
use netcdf, only: nf90_inq_varid
use netcdf, only: nf90_noerr
use mod_fv3_lola, only: fv3_h_to_ll,nxa,nya
use constants, only: grav
use constants, only: zero

implicit none

integer(i_kind),intent(in) :: it
real(r_kind),intent(in),dimension(:,:),pointer::ges_z
real(r_kind),intent(in),dimension(:,:),pointer::ges_t2m
real(r_kind),intent(in),dimension(:,:),pointer::ges_q2m
real(r_kind),intent(in),dimension(:,:),pointer::ges_howv ! --> howv
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remove the comment in Line 1851

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Will do , Thank you!

type (type_fv3regfilenameg),intent(in) :: fv3filenamegin
character(len=max_varname_length) :: name
integer(i_kind),allocatable,dimension(:):: dim
Expand All @@ -1835,6 +1862,9 @@ subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m)
integer(i_kind) kk,n,ns,j,ii,jj,mm1
character(len=:),allocatable :: sfcdata !='fv3_sfcdata'
character(len=:),allocatable :: dynvars !='fv3_dynvars'
! for checking the existence of howv in firstguess file
integer(i_kind) id_howv, iret_howv
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integer(i_kind) iret_bcast

! for io_layout > 1
real(r_kind),allocatable,dimension(:,:):: sfc_fulldomain
Expand All @@ -1850,6 +1880,9 @@ subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m)
allocate(work(itotsub*n2d))
allocate( sfcn2d(lat2,lon2,n2d))

!-- initialisation of the array for howv
sfcn2d(:,:,k_howv) = zero

if(mype==mype_2d ) then
allocate(sfc_fulldomain(nx,ny))

Expand Down Expand Up @@ -1877,6 +1910,19 @@ subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m)
iret=nf90_inquire_dimension(gfile_loc,k,name,len)
dim(k)=len
enddo

!--- check the existence of significant wave height (howv) in 2D FV3-LAM firstguess file
if ( i_howv_in_anav == 1 ) then
iret_howv = nf90_inq_varid(gfile_loc,'howv',id_howv)
if ( iret_howv /= nf90_noerr ) then
i_howv_in_data = 0 ! howv does not exist in firstguess
write(6,'(1x,A,1x,A,1x,A,1x,I4,1x,A,1x,I4.4,A)') 'subroutine gsi_fv3ncdf2d_read:: howv is NOT found in firstguess ', trim(sfcdata), ', iret = ',iret_howv, ' (on pe: ', mype,')'
else
i_howv_in_data = 1 ! howv is found in firstguess
write(6,'(1x,A,1x,A,1x,A,1x,I4,1x,I4,1x,A,1x,I4.4,A)') 'subroutine gsi_fv3ncdf2d_read:: Found howv in firstguess ', trim(sfcdata), ', iret, varid = ',iret_howv, id_howv,' (on pe: ', mype,')'
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we may NOT want to write out this information for each PE? Otherwise, it will be too many for runs using lots of PEs.

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These lines are done only on the PE which reads the surface firstguess, not by all the PEs. So only one PE prints this message. In the real run if GSI, it ddid show just one line in the "stdout" log file.

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I understand that for regional FV3 netcdf files, we use parallel I/O. You may check with @TingLei-NOAA whether parallel I/O applies to howv (if not yet, we may want to get it done in parallel, which will benefit the NA_3km domain)

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@guoqing-noaa Thanks for bringing out this point. For being now, in the parallel io for fv3-lam, these 2d fields are not considered ,which are still treated by subs like gsi_fv3net2d_read. In the future, when those 2d fields are more and more in the future, we may need to consider a similar parallelization to them.

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@TingLei-NOAA @guoqing-noaa
Thank you, Ting, for the explanation on this point.

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@TingLei-NOAA Thanks for the explanation. I think howv maybe the first 2D field to be read by regional GSI?
@GangZhao-NOAA it will be good if we can get the information about what extra minutes are needed to read the extra howv field for NA_3km domain. Thanks!

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@guoqing-noaa there are a group of 2d fields to be read in in gsi_fv3ncf2d_read and somes are written out through gsi_fv3ncdf_write_sfc in the current gsi.

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@TingLei-NOAA There is a subroutine gsi_fv3ncdf2d_read_v1(...) but it is never called anywhere. Do you have any idea what it is for? Thanks!

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@guoqing-noaa That is originally supposed to read some 2d fields from cold start files, while never actually implemented and used. It could be removed safely.

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@guoqing-noaa @TingLei-NOAA
As Ting answered, there are a bunch of 2d fields read from 2-D firstguess file (sfc_data.nc), including t2m, q2m and howv.

As for the "information about what extra minutes are needed to read the extra howv field for NA_3km domain", to be honest, I do not know. But the adding the analysis of howv (including reading firstguess, output analysis, read obs and cost function, minimisation, etc) does not increase the time cost much, even for 3km NA domain.
With my testing case on 3km NA domain, on Hera hybrid run (with gdas ensemble) without howv the wall-clock time is 973 seconds, with howv it is 974 seconds.

end if
end if

!!!!!!!!!!!! read in 2d variables !!!!!!!!!!!!!!!!!!!!!!!!!!
do i=ndimensions+1,nvariables
iret=nf90_inquire_variable(gfile_loc,i,name,len)
Expand Down Expand Up @@ -1904,6 +1950,8 @@ subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m)
k=k_t2m
else if( trim(name)=='Q2M'.or.trim(name)=='q2m' ) then
k=k_q2m
else if( trim(name)=='HOWV'.or.trim(name)=='howv' ) then ! howv (read if howv exists in firstguess, but no check on its existence.)
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remove comments in line 1953

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Will do. Thanks!

k=k_howv
else
cycle
endif
Expand Down Expand Up @@ -2036,6 +2084,8 @@ subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m)
if(allocated(sfc_fulldomain)) deallocate (sfc_fulldomain)
endif ! mype

!-- broadcast i_howv_in_data to all tasks (!!!!)
call mpi_bcast(i_howv_in_data, 1, mpi_itype, mype_2d, mpi_comm_world, iret_bcast)
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I don't understand why we need to broadcast i_howv_in_data? Should it be decided by each PE? Also I cannot think about a situation where one PE has HOWV data at firstguess while another PE doesn't?

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The task to read the surface fristguess data is done only by one PE, not by alll PEs, so "i_howv_in_data" is updated only on this specific PE. To use "i_howv_in_data" later on other PEs. it has to be broadcasts to all PEs.


!!!!!!! scatter !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
call mpi_scatterv(work,ijns2d,displss2d,mpi_rtype,&
Expand All @@ -2058,6 +2108,10 @@ subroutine gsi_fv3ncdf2d_read(fv3filenamegin,it,ges_z,ges_t2m,ges_q2m)
ges_t2m(:,:)=sfcn2d(:,:,k_t2m)
ges_q2m(:,:)=sfcn2d(:,:,k_q2m)
endif
if ( i_howv_in_anav == 1 ) then
ges_howv(:,:)=sfcn2d(:,:,k_howv) !howv: even no howv in firstguess, sfcn2d(:,:,k_howv)
! is still allocated and filled with initial values.
endif
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deallocate (sfcn2d,a)
return
end subroutine gsi_fv3ncdf2d_read
Expand Down Expand Up @@ -3131,6 +3185,8 @@ subroutine wrfv3_netcdf(fv3filenamegin)
! 2019-11-22 CAPS(C. Tong) - modify "add_saved" to properly output analyses
! 2021-01-05 x.zhang/lei - add code for updating delz analysis in regional da
! 2022-04-01 Y. Wang and X. Wang - add code for updating reflectivity
! 2023-07-30 Zhao - added code for the output of the analysis of
! significant wave height (howv)
!
! input argument list:
!
Expand Down Expand Up @@ -3173,6 +3229,7 @@ subroutine wrfv3_netcdf(fv3filenamegin)
real(r_kind),pointer,dimension(:,:,:):: ges_q =>NULL()
real(r_kind),pointer,dimension(:,: ):: ges_t2m =>NULL()
real(r_kind),pointer,dimension(:,: ):: ges_q2m =>NULL()
real(r_kind),pointer,dimension(:,: ):: ges_howv =>NULL() ! --> howv
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remove comments in Line 3232

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will do. Thanks!


integer(i_kind) i,k

Expand Down Expand Up @@ -3289,6 +3346,10 @@ subroutine wrfv3_netcdf(fv3filenamegin)
call GSI_BundleGetPointer (GSI_MetGuess_Bundle(it),'q2m',ges_q2m,istatus); ier=ier+istatus
call GSI_BundleGetPointer (GSI_MetGuess_Bundle(it),'t2m',ges_t2m,istatus );ier=ier+istatus
endif
!-- howv
if ( i_howv_in_anav == 1 ) then
call GSI_BundleGetPointer (GSI_MetGuess_Bundle(it),'howv',ges_howv,istatus); ier=ier+istatus
endif
if (ier/=0) call die('wrfv3_netcdf','cannot get pointers for fv3 met-fields, ier =',ier)

if (laeroana_fv3cmaq) then
Expand Down Expand Up @@ -3498,6 +3559,10 @@ subroutine wrfv3_netcdf(fv3filenamegin)
call gsi_fv3ncdf_write_sfc(fv3filenamegin,'t2m',ges_t2m,add_saved)
call gsi_fv3ncdf_write_sfc(fv3filenamegin,'q2m',ges_q2m,add_saved)
endif
!-- output analysis of howv only if howv is already in firstguess, i.e. i_howv_in_data = 1
if ( i_howv_in_anav == 1 .and. i_howv_in_data == 1 ) then
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call gsi_fv3ncdf_write_sfc(fv3filenamegin,'howv',ges_howv,add_saved)
endif

if(allocated(g_prsi)) deallocate(g_prsi)

Expand Down
15 changes: 13 additions & 2 deletions src/gsi/gsimod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,8 @@ module gsimod
i_coastline,i_gsdqc,qv_max_inc,ioption,l_precip_clear_only,l_fog_off,&
cld_bld_coverage,cld_clr_coverage,&
i_cloud_q_innovation,i_ens_mean,DTsTmax,&
i_T_Q_adjust,l_saturate_bkCloud,l_rtma3d,i_precip_vertical_check
i_T_Q_adjust,l_saturate_bkCloud,l_rtma3d,i_precip_vertical_check, &
corp_howv, hwllp_howv, l_tuneBE_howv
use gsi_metguess_mod, only: gsi_metguess_init,gsi_metguess_final
use gsi_chemguess_mod, only: gsi_chemguess_init,gsi_chemguess_final
use tcv_mod, only: init_tcps_errvals,tcp_refps,tcp_width,tcp_ermin,tcp_ermax
Expand Down Expand Up @@ -502,6 +503,9 @@ module gsimod
! 3. fv3_cmaq_regional = .true.
! 4. berror_fv3_cmaq_regional = .true.
! 09-15-2022 yokota - add scale/variable/time-dependent localization
! 2023-07-30 Zhao - added namelist options for analysis of significant wave height
! (aka howv in GSI code): corp_howv, hwllp_howv, l_tuneBE_howv
! (in namelist session rapidrefresh_cldsurf)
!
!EOP
!-------------------------------------------------------------------------
Expand Down Expand Up @@ -1558,6 +1562,12 @@ module gsimod
! = 2(clean Qg as in 1, and adjustment to the retrieved Qr/Qs/Qnr throughout the whole profile)
! = 3(similar to 2, but adjustment to Qr/Qs/Qnr only below maximum reflectivity level
! and where the dbz_obs is missing);
! corp_howv - real, static background error of howv (stddev error)
! = 0.42 meters (default)
! hwllp_howv - real, background error de-correlation length scale of howv
! = 170,000.0 meters (default 170 km)
! l_tuneBE_howv - logical, on/off the tuning of static BE of howv
! = .false. (default: turn off tuning the BE of howv)
!
namelist/rapidrefresh_cldsurf/dfi_radar_latent_heat_time_period, &
metar_impact_radius,metar_impact_radius_lowcloud, &
Expand All @@ -1578,7 +1588,8 @@ module gsimod
i_coastline,i_gsdqc,qv_max_inc,ioption,l_precip_clear_only,l_fog_off,&
cld_bld_coverage,cld_clr_coverage,&
i_cloud_q_innovation,i_ens_mean,DTsTmax, &
i_T_Q_adjust,l_saturate_bkCloud,l_rtma3d,i_precip_vertical_check
i_T_Q_adjust,l_saturate_bkCloud,l_rtma3d,i_precip_vertical_check, &
corp_howv, hwllp_howv, l_tuneBE_howv

! chem(options for gsi chem analysis) :
! berror_chem - .true. when background for chemical species that require
Expand Down
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