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For water tracers: Add handling of rank-3 fields and refactor med_phases_prep_glc_map_lnd2glc #634

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For water tracers: Add handling of rank-3 fields and refactor med_phases_prep_glc_map_lnd2glc #634

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6899f16
Generalize med_methods_mod to handle 2 ungridded dimensions
billsacks Feb 10, 2026
298f781
Use more efficient loop ordering in check_for_nans_2d
billsacks Feb 10, 2026
a7ded25
Extend med_io_mod to handle rank-3 fields
billsacks Feb 12, 2026
93cea3f
Minor cleanup
billsacks Feb 12, 2026
b2ff789
Add handling of rank-3 fields in med_map_field_normalized
billsacks Feb 21, 2026
2bec1cf
Refactor lnd2glc vertical interpolation
billsacks Feb 21, 2026
e9a26f4
Merge branch 'main' into handle_rank3_fields
billsacks Feb 25, 2026
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174 changes: 154 additions & 20 deletions mediator/med_io_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -729,7 +729,7 @@ subroutine med_io_write_FB(io_file, FB, whead, wdata, nx, ny, nt, &
type(ESMF_CoordSys_Flag) :: coordsys
integer :: rcode
integer :: nf,ns,ng
integer :: k,n
integer :: k,n,n2
integer :: ndims, nelements
integer ,target :: dimid2(2)
integer ,target :: dimid3(3)
Expand All @@ -754,15 +754,22 @@ subroutine med_io_write_FB(io_file, FB, whead, wdata, nx, ny, nt, &
integer, pointer :: Dof(:)
real(r8), pointer :: fldptr1(:)
real(r8), pointer :: fldptr2(:,:)
real(r8), pointer :: fldptr3(:,:,:)
real(r8), allocatable :: ownedElemCoords(:), ownedElemCoords_x(:), ownedElemCoords_y(:)
character(CS) :: cnumber
character(CS) :: cnumber2
character(CL) :: tmpstr
type(ESMF_Field) :: lfield
integer :: rank
integer :: ungriddedUBound(1) ! currently the size must equal 1 for rank 2 fields
integer :: gridToFieldMap(1) ! currently the size must equal 1 for rank 2 fields
logical :: tiles
character(CL), allocatable :: fieldNameList(:)

! For a single ungridded dimension, there will be 1 element in ungriddedUBound and 1
! element in gridToFieldMap; for two ungridded dimensions, there will be 2 elements in
! ungriddedUBound but still 1 element in gridToFieldMap.
integer :: ungriddedUBound(2)
integer :: gridToFieldMap(1)

character(*),parameter :: subName = '(med_io_write_FB) '
!-------------------------------------------------------------------------------

Expand Down Expand Up @@ -935,12 +942,47 @@ subroutine med_io_write_FB(io_file, FB, whead, wdata, nx, ny, nt, &

! TODO (mvertens, 2019-03-13): this is a temporary mod to NOT write hgt
if (trim(itemc) /= "hgt") then
if (rank == 2) then
if (rank == 3) then
call ESMF_FieldGet(lfield, ungriddedUBound=ungriddedUBound, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return
write(cnumber,'(i0)') ungriddedUbound(1)
write(cnumber2,'(i0)') ungriddedUbound(2)
call ESMF_LogWrite(trim(subname)//':'//'field '//trim(itemc)// &
' has an griddedUBound of '//trim(cnumber), ESMF_LOGMSG_INFO)
' has an ungriddedUBound of '//trim(cnumber)//' x '//trim(cnumber2), ESMF_LOGMSG_INFO)

! Create a new output variable for each element of the 2 ungridded dimensions
do n2 = 1,ungriddedUBound(2)
do n = 1,ungriddedUBound(1)
write(cnumber,'(i0)') n
write(cnumber2,'(i0)') n2
name1 = trim(lpre)//'_'//trim(itemc)//trim(cnumber)//'_'//trim(cnumber2)
call ESMF_LogWrite(trim(subname)//': defining '//trim(name1), ESMF_LOGMSG_INFO)
if (luse_float) then
rcode = pio_def_var(io_file, trim(name1), PIO_REAL, dimid, varid)
rcode = pio_put_att(io_file, varid,"_FillValue",real(lfillvalue,r4))
else
rcode = pio_def_var(io_file, trim(name1), PIO_DOUBLE, dimid, varid)
rcode = pio_put_att(io_file,varid,"_FillValue",lfillvalue)
end if
if (NUOPC_FieldDictionaryHasEntry(trim(itemc))) then
call NUOPC_FieldDictionaryGetEntry(itemc, canonicalUnits=cunit, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return
rcode = pio_put_att(io_file, varid, "units", trim(cunit))
end if
rcode = pio_put_att(io_file, varid, "standard_name", trim(name1))
if (present(tavg)) then
if (tavg) then
rcode = pio_put_att(io_file, varid, "cell_methods", "time: mean")
endif
endif
end do
end do
else if (rank == 2) then
call ESMF_FieldGet(lfield, ungriddedUBound=ungriddedUBound, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return
write(cnumber,'(i0)') ungriddedUbound(1)
call ESMF_LogWrite(trim(subname)//':'//'field '//trim(itemc)// &
' has an ungriddedUBound of '//trim(cnumber), ESMF_LOGMSG_INFO)

! Create a new output variable for each element of the undistributed dimension
do n = 1,ungriddedUBound(1)
Expand All @@ -958,7 +1000,7 @@ subroutine med_io_write_FB(io_file, FB, whead, wdata, nx, ny, nt, &
if (NUOPC_FieldDictionaryHasEntry(trim(itemc))) then
call NUOPC_FieldDictionaryGetEntry(itemc, canonicalUnits=cunit, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return
rcode = pio_put_att(io_file, varid, "units" , trim(cunit))
rcode = pio_put_att(io_file, varid, "units", trim(cunit))
end if
rcode = pio_put_att(io_file, varid, "standard_name", trim(name1))
if (present(tavg)) then
Expand All @@ -968,15 +1010,15 @@ subroutine med_io_write_FB(io_file, FB, whead, wdata, nx, ny, nt, &
endif
end if
end do
else
else if (rank == 1) then
name1 = trim(lpre)//'_'//trim(itemc)
call ESMF_LogWrite(trim(subname)//':'//trim(itemc)//':'//trim(name1),ESMF_LOGMSG_INFO)
call ESMF_LogWrite(trim(subname)//': defining '//trim(name1), ESMF_LOGMSG_INFO)
if (luse_float) then
rcode = pio_def_var(io_file, trim(name1), PIO_REAL, dimid, varid)
rcode = pio_put_att(io_file, varid, "_FillValue", real(lfillvalue, r4))
rcode = pio_put_att(io_file, varid,"_FillValue",real(lfillvalue,r4))
else
rcode = pio_def_var(io_file, trim(name1), PIO_DOUBLE, dimid, varid)
rcode = pio_put_att(io_file, varid, "_FillValue", lfillvalue)
rcode = pio_put_att(io_file,varid,"_FillValue",lfillvalue)
end if
if (NUOPC_FieldDictionaryHasEntry(trim(itemc))) then
call NUOPC_FieldDictionaryGetEntry(itemc, canonicalUnits=cunit, rc=rc)
Expand All @@ -988,7 +1030,10 @@ subroutine med_io_write_FB(io_file, FB, whead, wdata, nx, ny, nt, &
if (tavg) then
rcode = pio_put_att(io_file, varid, "cell_methods", "time: mean")
endif
end if
endif
else
call shr_log_error(subname//' ERROR: unhandled rank', line=__LINE__, file=u_FILE_u, rc=rc)
return
end if
end if
end do
Expand Down Expand Up @@ -1039,12 +1084,43 @@ subroutine med_io_write_FB(io_file, FB, whead, wdata, nx, ny, nt, &
end if

call FB_getFldPtr(FB, itemc, &
fldptr1=fldptr1, fldptr2=fldptr2, rank=rank, rc=rc)
fldptr1=fldptr1, fldptr2=fldptr2, fldptr3=fldptr3, rank=rank, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return

! TODO (mvertens, 2019-03-13): this is a temporary mod to NOT write hgt
if (trim(itemc) /= "hgt") then
if (rank == 2) then
if (rank == 3) then

! Determine the size of the ungridded dimensions and the index where the distributed dimension is located
call ESMF_FieldBundleGet(FB, itemc, field=lfield, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return
call ESMF_FieldGet(lfield, ungriddedUBound=ungriddedUBound, gridToFieldMap=gridToFieldMap, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return

if (gridToFieldMap(1) /= 3) then
call shr_log_error( &
subname//' ERROR: For rank-3 fields, currently only gridToFieldMap(1)==3 is supported', &
line=__LINE__, file=u_FILE_u, rc=rc)
return
end if

! Output for each combination of ungriddedUbound indices
do n2 = 1,ungriddedUBound(2)
do n = 1,ungriddedUBound(1)
write(cnumber,'(i0)') n
write(cnumber2,'(i0)') n2
name1 = trim(lpre)//'_'//trim(itemc)//trim(cnumber)//'_'//trim(cnumber2)
rcode = pio_inq_varid(io_file, trim(name1), varid)
call pio_setframe(io_file,varid,frame)

if (luse_float) then
call pio_write_darray(io_file, varid, iodesc, real(fldptr3(n,n2,:),r4), rcode, fillval=real(lfillvalue,r4))
else
call pio_write_darray(io_file, varid, iodesc, fldptr3(n,n2,:), rcode, fillval=lfillvalue)
end if
end do
end do
else if (rank == 2) then

! Determine the size of the ungridded dimension and the index where the undistributed dimension is located
call ESMF_FieldBundleGet(FB, itemc, field=lfield, rc=rc)
Expand Down Expand Up @@ -1489,7 +1565,7 @@ subroutine med_io_read_FB(filename, vm, FB, pre, frame, rc)
type(ESMF_Field) :: lfield
integer :: rcode
integer :: nf
integer :: k,n,l
integer :: k,n,n2,l
type(file_desc_t) :: pioid
type(var_desc_t) :: varid
type(io_desc_t) :: iodesc
Expand All @@ -1500,11 +1576,18 @@ subroutine med_io_read_FB(filename, vm, FB, pre, frame, rc)
integer :: rank, lsize
real(r8), pointer :: fldptr1(:), fldptr1_tmp(:)
real(r8), pointer :: fldptr2(:,:)
real(r8), pointer :: fldptr3(:,:,:)
character(CL) :: tmpstr
character(len=16) :: cnumber
character(len=16) :: cnumber2
integer(kind=Pio_Offset_Kind) :: lframe
integer :: ungriddedUBound(1) ! currently the size must equal 1 for rank 2 fieldds
integer :: gridToFieldMap(1) ! currently the size must equal 1 for rank 2 fieldds

! For a single ungridded dimension, there will be 1 element in ungriddedUBound and 1
! element in gridToFieldMap; for two ungridded dimensions, there will be 2 elements in
! ungriddedUBound but still 1 element in gridToFieldMap.
integer :: ungriddedUBound(2)
integer :: gridToFieldMap(1)

character(*),parameter :: subName = '(med_io_read_FB) '
!-------------------------------------------------------------------------------
rc = ESMF_Success
Expand Down Expand Up @@ -1569,7 +1652,9 @@ subroutine med_io_read_FB(filename, vm, FB, pre, frame, rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return
call ESMF_FieldGet(lfield, rank=rank, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return
if (rank == 2) then
if (rank == 3) then
name1 = trim(lpre)//'_'//trim(itemc)//'1_1'
else if (rank == 2) then
name1 = trim(lpre)//'_'//trim(itemc)//'1'
else if (rank == 1) then
name1 = trim(lpre)//'_'//trim(itemc)
Expand All @@ -1582,12 +1667,61 @@ subroutine med_io_read_FB(filename, vm, FB, pre, frame, rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return

! Get pointer to field bundle field
! Field bundle might be 2d or 1d - but field on mediator history or restart file will always be 1d
! Field bundle might be 3d, 2d or 1d - but field on mediator history or restart file will always be 1d
call FB_getFldPtr(FB, itemc, &
fldptr1=fldptr1, fldptr2=fldptr2, rank=rank, rc=rc)
fldptr1=fldptr1, fldptr2=fldptr2, fldptr3=fldptr3, rank=rank, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return

if (rank == 2) then
if (rank == 3) then

! Determine the size of the ungridded dimensions and the
! index where the distributed dimension is located
call ESMF_FieldBundleGet(FB, itemc, field=lfield, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return
call ESMF_FieldGet(lfield, ungriddedUBound=ungriddedUBound, gridToFieldMap=gridToFieldMap, rc=rc)
if (chkerr(rc,__LINE__,u_FILE_u)) return

if (gridToFieldMap(1) /= 3) then
call shr_log_error( &
subname//' ERROR: For rank-3 fields, currently only gridToFieldMap(1)==3 is supported', &
line=__LINE__, file=u_FILE_u, rc=rc)
return
end if

lsize = size(fldptr3, dim=3)
allocate(fldptr1_tmp(lsize))

do n2 = 1,ungriddedUBound(2)
do n = 1,ungriddedUBound(1)
! Create a name for the 1d field on the mediator history or restart file based on the
! ungridded dimension indices of the field bundle 3d field
write(cnumber,'(i0)') n
write(cnumber2,'(i0)') n2
name1 = trim(lpre)//'_'//trim(itemc)//trim(cnumber)//'_'//trim(cnumber2)

rcode = pio_inq_varid(pioid, trim(name1), varid)
if (rcode == pio_noerr) then
call ESMF_LogWrite(trim(subname)//' read field '//trim(name1), ESMF_LOGMSG_INFO)
if (chkerr(rc,__LINE__,u_FILE_u)) return
call pio_setframe(pioid, varid, lframe)
call pio_read_darray(pioid, varid, iodesc, fldptr1_tmp, rcode)
rcode = pio_get_att(pioid, varid, "_FillValue", lfillvalue)
if (rcode /= pio_noerr) then
lfillvalue = fillvalue
endif
do l = 1,size(fldptr1_tmp)
if (fldptr1_tmp(l) == lfillvalue) fldptr1_tmp(l) = 0.0_r8
enddo
else
fldptr1_tmp = 0.0_r8
endif
fldptr3(n,n2,:) = fldptr1_tmp(:)
end do
end do

deallocate(fldptr1_tmp)

else if (rank == 2) then

! Determine the size of the ungridded dimension and the
! index where the undistributed dimension is located
Expand Down
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