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Bugfixes #8

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merged 12 commits into from
Nov 15, 2019
Merged

Bugfixes #8

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e198c52
this PR includes: 1)vlab #69814: post update,2)ufs issue #3, Add 3D r…
junwang-noaa Nov 5, 2019
0e01f02
fix the add_dim interface
junwang-noaa Nov 6, 2019
d47965c
update gfslmp code changes from Ruiyu
junwang-noaa Nov 6, 2019
2d73753
update satmedmfvdifq from Jongil
junwang-noaa Nov 7, 2019
7e91866
update ccpp with gfdlmp change from Ruiyu
junwang-noaa Nov 7, 2019
3e01822
update idate and nfhours for iau
junwang-noaa Nov 10, 2019
94842bc
fix print line
junwang-noaa Nov 10, 2019
b71e959
initialize ihrst for ihrst
junwang-noaa Nov 10, 2019
2eb8b2c
initialize ihrst for inline post
junwang-noaa Nov 11, 2019
248196c
add comments for write grid comp idate change when iau is enabled
junwang-noaa Nov 12, 2019
bddc70c
update fv3 dycore and ccpp physics repo
junwang-noaa Nov 15, 2019
97d12bc
checkout out dev/emc from EMC fv3 dycore repo and master branch in NC…
junwang-noaa Nov 15, 2019
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7 changes: 4 additions & 3 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
[submodule "atmos_cubed_sphere"]
path = atmos_cubed_sphere
url = https://github.com/NOAA-EMC/GFDL_atmos_cubed_sphere
branch = dev/emc
url = https://github.com/junwang-noaa/GFDL_atmos_cubed_sphere
branch = regfv3_rst
[submodule "ccpp/framework"]
path = ccpp/framework
url = https://github.com/NCAR/ccpp-framework
[submodule "ccpp/physics"]
path = ccpp/physics
url = https://github.com/NCAR/ccpp-physics
url = https://github.com/junwang-noaa/ccpp-physics
branch = gfdlmp_update
2 changes: 1 addition & 1 deletion atmos_cubed_sphere
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Submodule atmos_cubed_sphere updated 1 files
+6 −0 model/fv_regional_bc.F90
2 changes: 1 addition & 1 deletion ccpp/physics
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Submodule physics updated 1 files
+4 −4 physics/module_gfdl_cloud_microphys.F90
2 changes: 1 addition & 1 deletion gfsphysics/GFS_layer/GFS_physics_driver.F90
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Expand Up @@ -1149,7 +1149,7 @@ subroutine GFS_physics_driver &
if (fice(i) < one) then
wet(i) = .true.
! Sfcprop%tsfco(i) = tgice
Sfcprop%tsfco(i) = max(Sfcprop%tisfc(i), tgice)
if (.not. Model%cplflx) Sfcprop%tsfco(i) = max(Sfcprop%tisfc(i), tgice)
! Sfcprop%tsfco(i) = max((Sfcprop%tsfc(i) - fice(i)*sfcprop%tisfc(i)) &
! / (one - fice(i)), tgice)
endif
Expand Down
11 changes: 10 additions & 1 deletion gfsphysics/GFS_layer/GFS_restart.F90
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Expand Up @@ -117,6 +117,9 @@ subroutine GFS_restart_populate (Restart, Model, Statein, Stateout, Sfcprop, &
#endif

Restart%num3d = Model%ntot3d
if(Model%lrefres) then
Restart%num3d = Model%ntot3d+1
endif
#ifdef CCPP
! GF
if (Model%imfdeepcnv == 3) then
Expand Down Expand Up @@ -252,7 +255,13 @@ subroutine GFS_restart_populate (Restart, Model, Statein, Stateout, Sfcprop, &
Restart%data(nb,num)%var3p => Tbd(nb)%phy_f3d(:,:,num)
enddo
enddo

if (Model%lrefres) then
num = Model%ntot3d+1
restart%name3d(num) = 'ref_f3d'
do nb = 1,nblks
Restart%data(nb,num)%var3p => IntDiag(nb)%refl_10cm(:,:)
enddo
endif
#ifdef CCPP
!--- RAP/HRRR-specific variables, 3D
num = Model%ntot3d
Expand Down
12 changes: 11 additions & 1 deletion gfsphysics/GFS_layer/GFS_typedefs.F90
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Expand Up @@ -701,6 +701,9 @@ module GFS_typedefs
!--- GFDL microphysical paramters
logical :: lgfdlmprad !< flag for GFDL mp scheme and radiation consistency

!--- Thompson,GFDL mp parameter
logical :: lrefres !< flag for radar reflectivity in restart file

!--- land/surface model parameters
integer :: lsm !< flag for land surface model lsm=1 for noah lsm
integer :: lsm_noah=1 !< flag for NOAH land surface model
Expand Down Expand Up @@ -2740,6 +2743,9 @@ subroutine control_initialize (Model, nlunit, fn_nml, me, master, &
!--- GFDL microphysical parameters
logical :: lgfdlmprad = .false. !< flag for GFDLMP radiation interaction

!--- Thompson,GFDL microphysical parameter
logical :: lrefres = .false. !< flag for radar reflectivity in restart file

!--- land/surface model parameters
integer :: lsm = 1 !< flag for land surface model to use =0 for osu lsm; =1 for noah lsm; =2 for noah mp lsm; =3 for RUC lsm
integer :: lsoil = 4 !< number of soil layers
Expand Down Expand Up @@ -3023,7 +3029,7 @@ subroutine control_initialize (Model, nlunit, fn_nml, me, master, &
mg_do_graupel, mg_do_hail, mg_nccons, mg_nicons, mg_ngcons, &
mg_ncnst, mg_ninst, mg_ngnst, sed_supersat, do_sb_physics, &
mg_alf, mg_qcmin, mg_do_ice_gmao, mg_do_liq_liu, &
ltaerosol, lradar, ttendlim, lgfdlmprad, &
ltaerosol, lradar, lrefres, ttendlim, lgfdlmprad, &
!--- max hourly
avg_max_length, &
!--- land/surface model control
Expand Down Expand Up @@ -3312,6 +3318,8 @@ subroutine control_initialize (Model, nlunit, fn_nml, me, master, &
Model%ttendlim = ttendlim
!--- gfdl MP parameters
Model%lgfdlmprad = lgfdlmprad
!--- Thompson,GFDL MP parameter
Model%lrefres = lrefres

!--- land/surface model parameters
Model%lsm = lsm
Expand Down Expand Up @@ -4310,6 +4318,7 @@ subroutine control_print(Model)
print *, ' Thompson microphysical parameters'
print *, ' ltaerosol : ', Model%ltaerosol
print *, ' lradar : ', Model%lradar
print *, ' lrefres : ', Model%lrefres
print *, ' ttendlim : ', Model%ttendlim
print *, ' '
endif
Expand All @@ -4327,6 +4336,7 @@ subroutine control_print(Model)
if (Model%imp_physics == Model%imp_physics_gfdl) then
print *, ' GFDL microphysical parameters'
print *, ' GFDL MP radiation inter: ', Model%lgfdlmprad
print *, ' lrefres : ', Model%lrefres
print *, ' '
endif

Expand Down
8 changes: 4 additions & 4 deletions gfsphysics/physics/gfdl_cloud_microphys.F90
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Expand Up @@ -4688,7 +4688,7 @@ subroutine cloud_diagnosis (is, ie, ks, ke, den, delp, lsm, qmw, qmi, qmr, qms,
real :: n0r = 8.0e6, n0s = 3.0e6, n0g = 4.0e6
real :: alphar = 0.8, alphas = 0.25, alphag = 0.5
real :: gammar = 17.837789, gammas = 8.2850630, gammag = 11.631769
real :: qmin = 1.0e-12, beta = 1.22
real :: qmin = 1.0e-12, beta = 1.22, qmin1 = 9.e-6

do k = ks, ke
do i = is, ie
Expand Down Expand Up @@ -4718,7 +4718,7 @@ subroutine cloud_diagnosis (is, ie, ks, ke, den, delp, lsm, qmw, qmi, qmr, qms,
! cloud ice (Heymsfield and Mcfarquhar, 1996)
! -----------------------------------------------------------------------

if (qmi (i, k) .gt. qmin) then
if (qmi (i, k) .gt. qmin1) then
qci (i, k) = dpg * qmi (i, k) * 1.0e3
rei_fac = log (1.0e3 * qmi (i, k) * den (i, k))
if (t (i, k) - tice .lt. - 50) then
Expand All @@ -4744,7 +4744,7 @@ subroutine cloud_diagnosis (is, ie, ks, ke, den, delp, lsm, qmw, qmi, qmr, qms,
! cloud ice (Wyser, 1998)
! -----------------------------------------------------------------------

if (qmi (i, k) .gt. qmin) then
if (qmi (i, k) .gt. qmin1) then
qci (i, k) = dpg * qmi (i, k) * 1.0e3
bw = - 2. + 1.e-3 * log10 (den (i, k) * qmi (i, k) / rho_0) * max (0.0, tice - t (i, k)) ** 1.5
rei (i, k) = 377.4 + bw * (203.3 + bw * (37.91 + 2.3696 * bw))
Expand Down Expand Up @@ -4774,7 +4774,7 @@ subroutine cloud_diagnosis (is, ie, ks, ke, den, delp, lsm, qmw, qmi, qmr, qms,
! snow (Lin et al., 1983)
! -----------------------------------------------------------------------

if (qms (i, k) .gt. qmin) then
if (qms (i, k) .gt. qmin1) then
qcs (i, k) = dpg * qms (i, k) * 1.0e3
lambdas = exp (0.25 * log (pi * rhos * n0s / qms (i, k) / den (i, k)))
res (i, k) = 0.5 * exp (log (gammas / 6) / alphas) / lambdas * 1.0e6
Expand Down
53 changes: 27 additions & 26 deletions gfsphysics/physics/satmedmfvdifq.f
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Expand Up @@ -151,7 +151,7 @@ subroutine satmedmfvdifq(ix,im,km,ntrac,ntcw,ntiw,ntke,
& rlmn, rlmn1, rlmx, elmx,
& ttend, utend, vtend, qtend,
& zfac, zfmin, vk, spdk2,
& tkmin, xkzinv, xkgdx,
& tkmin, tkminx, xkzinv, xkgdx,
& zlup, zldn, bsum,
& tem, tem1, tem2,
& ptem, ptem0, ptem1, ptem2
Expand All @@ -176,11 +176,11 @@ subroutine satmedmfvdifq(ix,im,km,ntrac,ntcw,ntiw,ntke,
parameter(prmin=0.25,prmax=4.0)
parameter(pr0=1.0,prtke=1.0,prscu=0.67)
parameter(f0=1.e-4,crbmin=0.15,crbmax=0.35)
parameter(tkmin=1.e-9,dspmax=10.0)
parameter(tkmin=1.e-9,tkminx=0.2,dspmax=10.0)
parameter(qmin=1.e-8,qlmin=1.e-12,zfmin=1.e-8)
parameter(aphi5=5.,aphi16=16.)
parameter(elmfac=1.0,elefac=1.0,cql=100.)
parameter(dw2min=1.e-4,dkmax=1000.,xkgdx=25000.)
parameter(dw2min=1.e-4,dkmax=1000.,xkgdx=5000.)
parameter(qlcr=3.5e-5,zstblmax=2500.,xkzinv=0.1)
parameter(h1=0.33333333)
parameter(ck0=0.4,ck1=0.15,ch0=0.4,ch1=0.15)
Expand Down Expand Up @@ -273,20 +273,20 @@ subroutine satmedmfvdifq(ix,im,km,ntrac,ntcw,ntiw,ntke,
xkzo(i,k) = 0.0
xkzmo(i,k) = 0.0
if (k < kinver(i)) then
! vertical background diffusivity
ptem = prsi(i,k+1) * tx1(i)
tem1 = 1.0 - ptem
tem2 = tem1 * tem1 * 10.0
tem2 = min(1.0, exp(-tem2))
xkzo(i,k) = xkzm_hx(i) * tem2
!
! minimum turbulent mixing length
ptem = prsl(i,k) * tx1(i)
tem1 = 1.0 - ptem
tem2 = tem1 * tem1 * 2.5
tem2 = min(1.0, exp(-tem2))
rlmnz(i,k)= rlmn * tem2
rlmnz(i,k)= max(rlmnz(i,k), rlmn1)
! vertical background diffusivity for momentum
! vertical background diffusivity
ptem = prsi(i,k+1) * tx1(i)
tem1 = 1.0 - ptem
tem2 = tem1 * tem1 * 10.0
tem2 = min(1.0, exp(-tem2))
xkzo(i,k) = xkzm_hx(i) * tem2
! vertical background diffusivity for momentum
if (ptem >= xkzm_s) then
xkzmo(i,k) = xkzm_mx(i)
kx1(i) = k + 1
Expand Down Expand Up @@ -674,20 +674,20 @@ subroutine satmedmfvdifq(ix,im,km,ntrac,ntcw,ntiw,ntke,
!
! background diffusivity decreasing with increasing surface layer stability
!
do i = 1, im
if(.not.sfcflg(i)) then
tem = (1. + 5. * rbsoil(i))**2.
! tem = (1. + 5. * zol(i))**2.
frik(i) = 0.1 + 0.9 / tem
endif
enddo
!
do k = 1,km1
do i=1,im
xkzo(i,k) = frik(i) * xkzo(i,k)
xkzmo(i,k)= frik(i) * xkzmo(i,k)
enddo
enddo
! do i = 1, im
! if(.not.sfcflg(i)) then
! tem = (1. + 5. * rbsoil(i))**2.
!! tem = (1. + 5. * zol(i))**2.
! frik(i) = 0.1 + 0.9 / tem
! endif
! enddo
!
! do k = 1,km1
! do i=1,im
! xkzo(i,k) = frik(i) * xkzo(i,k)
! xkzmo(i,k)= frik(i) * xkzmo(i,k)
! enddo
! enddo
!
! The background vertical diffusivities in the inversion layers are limited
! to be less than or equal to xkzminv
Expand Down Expand Up @@ -867,13 +867,14 @@ subroutine satmedmfvdifq(ix,im,km,ntrac,ntcw,ntiw,ntke,
do i = 1, im
if(k == 1) then
tem = ckz(i,1)
tem1 = xkzmo(i,1)
tem1 = 0.5 * xkzmo(i,1)
else
tem = 0.5 * (ckz(i,k-1) + ckz(i,k))
tem1 = 0.5 * (xkzmo(i,k-1) + xkzmo(i,k))
endif
ptem = tem1 / (tem * elm(i,k))
tkmnz(i,k) = ptem * ptem
tkmnz(i,k) = min(tkmnz(i,k), tkminx)
tkmnz(i,k) = max(tkmnz(i,k), tkmin)
enddo
enddo
Expand Down
9 changes: 2 additions & 7 deletions io/FV3GFS_io.F90
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Expand Up @@ -1119,15 +1119,10 @@ subroutine sfc_prop_restart_read (Sfcprop, Atm_block, Model, fv_domain)
Sfcprop(nb)%zorll(ix) = Sfcprop(nb)%zorlo(ix)
Sfcprop(nb)%zorl(ix) = Sfcprop(nb)%zorlo(ix)
Sfcprop(nb)%tsfc(ix) = Sfcprop(nb)%tsfco(ix)
if (Sfcprop(nb)%slmsk(ix) < 0.1 .or. Sfcprop(nb)%slmsk(ix) > 1.9) then
if (Sfcprop(nb)%slmsk(ix) > 1.9) then
Sfcprop(nb)%landfrac(ix) = 0.0
if (Sfcprop(nb)%oro_uf(ix) > 0.01) then
Sfcprop(nb)%lakefrac(ix) = 1.0 ! lake
else
Sfcprop(nb)%lakefrac(ix) = 0.0 ! ocean
endif
else
Sfcprop(nb)%landfrac(ix) = 1.0 ! land
Sfcprop(nb)%landfrac(ix) = Sfcprop(nb)%slmsk(ix)
endif
enddo
enddo
Expand Down
67 changes: 40 additions & 27 deletions io/module_wrt_grid_comp.F90
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Expand Up @@ -71,6 +71,7 @@ module module_wrt_grid_comp
logical,save :: first_init=.false.
logical,save :: first_run=.false.
logical,save :: first_getlatlon=.true.
logical,save :: change_wrtidate=.false.
!
!-----------------------------------------------------------------------
!
Expand Down Expand Up @@ -173,7 +174,8 @@ subroutine wrt_initialize(wrt_comp, imp_state_write, exp_state_write, clock, rc)
real(ESMF_KIND_R4) :: valueR4
real(ESMF_KIND_R8) :: valueR8

integer :: attCount, axeslen, jidx, noutfile
integer :: attCount, axeslen, jidx, idx, noutfile
character(19) :: newdate
character(128) :: FBlist_outfilename(100), outfile_name
character(128),dimension(:,:), allocatable :: outfilename
real(8), dimension(:), allocatable :: slat
Expand All @@ -183,7 +185,6 @@ subroutine wrt_initialize(wrt_comp, imp_state_write, exp_state_write, clock, rc)
real(ESMF_KIND_R8) :: geo_lon, geo_lat
real(ESMF_KIND_R8) :: lon1_r8, lat1_r8
real(ESMF_KIND_R8) :: x1, y1, x, y
type(ESMF_Time) :: IO_BASETIME_IAU
type(ESMF_TimeInterval) :: IAU_offsetTI
type(ESMF_DataCopy_Flag) :: copyflag=ESMF_DATACOPY_REFERENCE
! real(8),parameter :: PI=3.14159265358979d0
Expand Down Expand Up @@ -469,8 +470,32 @@ subroutine wrt_initialize(wrt_comp, imp_state_write, exp_state_write, clock, rc)
call ESMF_Finalize(endflag=ESMF_END_ABORT)

endif
!
!-----------------------------------------------------------------------
!*** get write grid component initial time from clock
!-----------------------------------------------------------------------
!
call ESMF_ClockGet(clock =CLOCK & !<-- The ESMF Clock
,startTime=wrt_int_state%IO_BASETIME & !<-- The Clock's starting time
,rc =RC)


call ESMF_TimeGet(time=wrt_int_state%IO_BASETIME,yy=idate(1),mm=idate(2),dd=idate(3),h=idate(4), &
m=idate(5),s=idate(6),rc=rc)
! if (lprnt) write(0,*) 'in wrt initial, io_baseline time=',idate,'rc=',rc
idate(7) = 1
wrt_int_state%idate = idate
wrt_int_state%fdate = idate
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@jswhit2 jswhit2 Nov 12, 2019 •
edited
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add a comment here since it's not obvious what's going on. Something like "update idate when IAU is enabled to reference center of IAU window"

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Added comments "! update IO-BASETIME and idate on write grid comp when IAU is enabled"

! update IO-BASETIME and idate on write grid comp when IAU is enabled
if(iau_offset > 0 ) then
call ESMF_TimeIntervalSet(IAU_offsetTI, h=iau_offset, rc=rc)
wrt_int_state%IO_BASETIME = wrt_int_state%IO_BASETIME + IAU_offsetTI
call ESMF_TimeGet(time=wrt_int_state%IO_BASETIME,yy=idate(1),mm=idate(2),dd=idate(3),h=idate(4), &
m=idate(5),s=idate(6),rc=rc)
wrt_int_state%idate = idate
change_wrtidate = .true.
if (lprnt) print *,'in wrt initial, with iau, io_baseline time=',idate,'rc=',rc
endif
!
! Create field bundle
!-------------------------------------------------------------------
!
Expand Down Expand Up @@ -867,6 +892,17 @@ subroutine wrt_initialize(wrt_comp, imp_state_write, exp_state_write, clock, rc)

if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return

! update the time:units when idate on write grid component is changed
if ( index(trim(attNameList(i)),'time:units')>0) then
if ( change_wrtidate ) then
idx = index(trim(valueS),' since ')
if(lprnt) print *,'in write grid comp, time:unit=',trim(valueS)
write(newdate,'(I4.4,a,I2.2,a,I2.2,a,I2.2,a,I2.2,a,I2.2)') idate(1),'-', &
idate(2),'-',idate(3),' ',idate(4),':',idate(5),':',idate(6)
valueS = valueS(1:idx+6)//newdate
if(lprnt) print *,'in write grid comp, new time:unit=',trim(valueS)
endif
endif
call ESMF_AttributeSet(wrtgrid, convention="NetCDF", purpose="FV3", &
name=trim(attNameList(i)), value=valueS, rc=rc)

Expand Down Expand Up @@ -1036,28 +1072,6 @@ subroutine wrt_initialize(wrt_comp, imp_state_write, exp_state_write, clock, rc)
if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return
!
!-----------------------------------------------------------------------
!*** SET THE IO_BaseTime TO THE INITIAL CLOCK TIME.
!-----------------------------------------------------------------------
!
call ESMF_ClockGet(clock =CLOCK & !<-- The ESMF Clock
,startTime=wrt_int_state%IO_BASETIME & !<-- The Clock's starting time
,rc =RC)

call ESMF_TimeGet(time=wrt_int_state%IO_BASETIME,yy=idate(1),mm=idate(2),dd=idate(3),h=idate(4), &
m=idate(5),s=idate(6),rc=rc)
! if (lprnt) write(0,*) 'in wrt initial, io_baseline time=',idate,'rc=',rc
idate(7) = 1
wrt_int_state%idate = idate
wrt_int_state%fdate = idate
if(iau_offset > 0 ) then
call ESMF_TimeIntervalSet(IAU_offsetTI, h=iau_offset, rc=rc)
IO_BASETIME_IAU = wrt_int_state%IO_BASETIME + IAU_offsetTI
call ESMF_TimeGet(time=IO_BASETIME_IAU,yy=idate(1),mm=idate(2),dd=idate(3),h=idate(4), &
m=idate(5),s=idate(6),rc=rc)
! if (lprnt) write(0,*) 'in wrt initial, with iau, io_baseline time=',idate,'rc=',rc
endif
!
!-----------------------------------------------------------------------
!*** SET THE FIRST HISTORY FILE'S TIME INDEX.
!-----------------------------------------------------------------------
!
Expand Down Expand Up @@ -1250,10 +1264,9 @@ subroutine wrt_run(wrt_comp, imp_state_write, exp_state_write,clock,rc)
! 'nseconds_num=',nseconds_num,nseconds_den,'mype=',mype
!
nf_seconds = nf_hours*3600+nf_minuteS*60+nseconds+real(nseconds_num)/real(nseconds_den)
! shift forecast hour by iau_offset if iau is on.
nf_seconds = nf_seconds - iau_offset*3600
wrt_int_state%nfhour = nf_seconds/3600.
nf_hours = int(nf_seconds/3600.)
if(mype == lead_write_task) print *,'in write grid comp, nf_hours=',nf_hours
! if iau_offset > nf_hours, don't write out anything
if (nf_hours < 0) return

Expand Down
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