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Rtofs ufs cycle updates #106

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d838629
modifications for mom6 incremental update nc file
zgarraffo Jan 15, 2026
9518a49
leave exrtofs_glo_ncoda_hycom_var.sh as in develop
zgarraffo Jan 15, 2026
3050391
Merge branch 'develop' into rtofs_ufs_cycle_updates
zgarraffo Jan 15, 2026
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6 changes: 4 additions & 2 deletions parm/rtofs_glo_ncoda_inc2mom6nc_lyr.input
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,11 @@ MOM.res_3.nc
MOM.res_4.nc
&TShincname
&UVincname
&IDM 'idm ' = longitudinal array size
&JDM 'jdm ' = latitudinal array size
&IDM 'ii ' = longitudinal array size
&JDM 'jj ' = latitudinal array size
&KDM 'kk ' = number of layers restart
1324 'itest ' = longitudinal test point (optional, default 0)
1898 'jtest ' = latitudinal test point (optional, default 0)
&KDM 'kncoda' = number of NCODA levels equal to kk for layer increments
0.50 'zl ' = nominal depth of layer 1 from MOM archive
1.90 'zl ' = nominal depth of layer 2
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1 change: 0 additions & 1 deletion scripts/exrtofs_glo_ncoda_hycom_var.sh
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Expand Up @@ -92,7 +92,6 @@ cat << eof1 > odsetnl
&end
eof1

# kkm, kko, m, and n can be pulled from parm blkdat.input
cat << eof2 > ogridnl
&gridnl
delx(1) = 8896.78809,
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44 changes: 23 additions & 21 deletions scripts/exrtofs_glo_ncoda_inc.sh
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Expand Up @@ -42,13 +42,13 @@ echo dtg12 $dtg $dtgm1 $dtgm2
mode=incup
#inputgrid=0.08, change to 0p08
reg=GLB
DEPTH_FILE=${FIXrtofs}/depth_${reg}${inputgrid}_09m11ob2_mom6.nc
DEPTH_FILE=${FIXrtofs}/depth_${reg}.${inputgrid}_09m11ob2_mom6.nc
IDM=$(ncdump -h ${DEPTH_FILE} | grep 'nx =' | cut -d' ' -f3)
JDM=$(ncdump -h ${DEPTH_FILE} | grep 'ny =' | cut -d' ' -f3)
KDM=41 # or get from restart file?
SIZN="${IDM}x${JDM}"

ln -f -s ${FIXrtofs}/depth_${reg}.${inputgrid}_09m11ob2_mom6.nc .
ln -f -s ${FIXrtofs}/depth_${reg}.${inputgrid}_09m11ob2_mom6.nc depth_GLBb0.08_09m11ob2_mom6.nc
ln -f -s ${FIXrtofs}/regional.mom6.nc .

# 2. link to ncoda hycom var restart files
Expand All @@ -66,8 +66,8 @@ export vvelinc=vvel_${dtg}_analinc
export lyrthbg=lyrthk_${dtgm1}_fcstfld

#names can be changed. Names in INPUT will be MOM.inc.TSzh.nc, MOM.inc.UV.nc
export TShar=MOM.res_Y${jday:0:4}_D${jday:4:3}_S00000_inc.TSzh.nc
export UVar=MOM.res_Y${jday:0:4}_D${jday:4:3}_S00000_inc.TSzh.nc
export TShinc=MOM.res_Y${jday:0:4}_D${jday:4:3}_S00000_inc.TSzh.nc
export UVinc=MOM.res_Y${jday:0:4}_D${jday:4:3}_S00000_inc.UV.nc

# Check for the existence of analysis increment files
# These are needed to create the HYCOM incremental update file
Expand Down Expand Up @@ -108,48 +108,50 @@ else
fi

# Link the MOM6 template restart files
if [ -e $COMINm1/RESTART/${dtg:0:8}_000000.MOM.res.nc]; then
ln -sf $COMINm1/RESTART/${dtg:0:8}_000000.MOM.res.nc MOM.res.nc
if [ -e $COMINm1/RESTART/${dtg:0:8}.000000.MOM.res.nc ]; then
ln -sf $COMINm1/RESTART/${dtg:0:8}.000000.MOM.res.nc MOM.res.nc
else
msg="$COMINm1/${dtg:0:8}_000000.MOM.res.nc is missing"
msg="$COMINm1/RESTART/${dtg:0:8}.000000.MOM.res.nc is missing"
err_exit $msg
fi
if [ -e $COMINm1/RESTART/${dtg:0:8}_000000.MOM.res_1.nc]; then
ln -sf $COMINm1/RESTART/${dtg:0:8}_000000.MOM_1.res.nc MOM.res.nc
if [ -e $COMINm1/RESTART/${dtg:0:8}.000000.MOM.res_1.nc ]; then
ln -sf $COMINm1/RESTART/${dtg:0:8}.000000.MOM.res_1.nc MOM.res_1.nc
else
msg="$COMINm1/${dtg:0:8}_000000.MOM_1.res.nc is missing"
msg="$COMINm1/RESTART/${dtg:0:8}.000000.MOM.res_1.nc is missing"
err_exit $msg
fi
if [ -e $COMINm1/RESTART/${dtg:0:8}_000000.MOM_3.res.nc]; then
ln -sf $COMINm1/RESTART/${dtg:0:8}_000000.MOM_3.res.nc MOM.res.nc
if [ -e $COMINm1/RESTART/${dtg:0:8}.000000.MOM.res_3.nc ]; then
ln -sf $COMINm1/RESTART/${dtg:0:8}.000000.MOM.res_3.nc MOM.res_3.nc
else
msg="$COMINm1/${dtg:0:8}_000000.MOM_3.res.nc is missing"
msg="$COMINm1/RESTART/${dtg:0:8}.000000.MOM.res_3.nc is missing"
err_exit $msg
fi
if [ -e $COMINm1/RESTART/${dtg:0:8}_000000.MOM_4.res.nc]; then
ln -sf $COMINm1/RESTART/${dtg:0:8}_000000.MOM_4.res.nc MOM.res.nc
if [ -e $COMINm1/RESTART/${dtg:0:8}.000000.MOM.res_4.nc ]; then
ln -sf $COMINm1/RESTART/${dtg:0:8}.000000.MOM.res_4.nc MOM.res_4.nc
else
msg="$COMINm1/${dtg:0:8}_000000.MOM_4.res.nc is missing"
msg="$COMINm1/RESTART/${dtg:0:8}.000000.MOM.res_4.nc is missing"
err_exit $msg
fi


# copy modify input file with local vars
cp ${PARMrtofs}/${RUN}_${modID}.ncoda_inc2mom6nc.input ./ncoda_inc2mom6nc.input
sed -i -e "s/&TShincname/$TShar/" \
-e "s/&UVincname/$UVar/" \
cp ${PARMrtofs}/${RUN}_${modID}_ncoda_inc2mom6nc_lyr.input ./ncoda_inc2mom6nc_lyr.input
sed -i -e "s/&TShincname/$TShinc/g" \
-e "s/&UVincname/$UVinc/g" \
-e "s/&IDM/$IDM/g" \
-e "s/&JDM/$JDM/g" \
-e "s/&KDM/$KDM/g" \
-e "s/&seatmpinc/${tempinc}/g" \
-e "s/&salintinc/${salininc}/g" \
-e "s/&uvelinc/${uvelinc}/g" \
-e "s/&vvelinc/${vvelinc}/g" \
-e "s/&lyrthknam/${lyrthbg}" \
-e "s/&lyrthkname/${lyrthbg}/g" ./ncoda_inc2mom6nc_lyr.input

$EXECrtofs/rtofs_ncodaz_inc2mom6nc_glb_lyr.x < ncoda_inc2mom6nc_lyr.input >> $pgmout
err=$?; export err ; err_chk
echo " error from rtofs_ncodaz_inc2mom6nc_glb_lyr=",$err
cp $TShinc $COMOUT/rtofs_glo.$TShinc
cp $UVinc $COMOUT/rtofs_glo.$UVinc


msg="THE RTOFS_GLO_NCODA_INC JOB HAS ENDED NORMALLY on $(hostname) at $(date)"
postmsg "$msg"
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3 changes: 3 additions & 0 deletions sorc/hycom_tools_for_mom6.fd/build_all.sh
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Expand Up @@ -12,6 +12,9 @@ source ${BASE}/load_modules.sh ${dir_mod0}
make all

# move executables
for f in `ls -1 *.x`; do
cp $f ../../exec/rtofs_$f
done
mkdir -p ${BASE}/exec
mv *.x ${BASE}/exec

Expand Down
19 changes: 12 additions & 7 deletions sorc/hycom_tools_for_mom6.fd/ncodaz_inc2mom6nc_glb_lyr.f
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Expand Up @@ -174,10 +174,17 @@ program ncodaz_inc2mom6nc_glb
c --- 'flnm_p' = name of ncoda density displacement file, or "NONE"
c --- 'flnm_h' = name of the background field layer thick. as ncoda binary

c itest,jtest show be read with blkini2, now hard coded
itest=1324
jtest=1898
call blkini(kncoda,'kncoda')
call blkini2(i,j,'itest ','kncoda')
if (j.eq.1) then
itest = i
call blkini(jtest, 'jtest ')
call blkini(kncoda, 'kncoda')
else
itest = 0
jtest = 0
kncoda = i
endif

if (kncoda.ne.kk) then
write(6,*)'error, kncoda has to be kk for lyr option'
stop
Expand Down Expand Up @@ -217,9 +224,7 @@ program ncodaz_inc2mom6nc_glb
read (*,'(a)') flnm_p
write (lp,'(2a)') 'Pncoda file: ',trim(flnm_p)
read (*,'(a)') flnm_h
write (lp,'(2a)') 'h background file: ',trim(flnm_p)
read (*,'(a)') flnm_h
write (lp,'(2a)') 'h background file: ',trim(flnm_h)rite (lp,'(2a)') 'h background file: ',trim(flnm_h)
write (lp,'(2a)') 'h background file: ',trim(flnm_h)

C

Expand Down