#!/bin/csh
#
# --- extract 2-d fields from a single HYCOM archive file.
# --- configured for 22 layers.
#
# --- output is netCDF.
# --- this is an example, customize it for your datafile needs.
#
#
# --- optional title and institution.
#
# Check that the neccesary variables are sourced, otherwise try to source them
#if (-e ${HYCOMDIR}/ALL/scripts/sourceall.src) then
# source ${HYCOMDIR}/ALL/scripts/sourceall.src
#else
# echo 'warning: sourceall.src not in expected location. Sourcing has possibly failed'
#endif
#if (-e /opt/modules/modules/init/csh) then #We are on aster
# source /opt/modules/modules/init/csh
# module load nco-3.0.0
#endif
# Get the thbase and yrflag value from blkdat.input
setenv THB `grep \'thbase blkdat.input | awk '{print $1}'`
setenv YRF `grep \'yrflag blkdat.input | awk '{print $1}'`
setenv IDM `grep \'idm blkdat.input | awk '{print $1}'`
setenv JDM `grep \'jdm blkdat.input | awk '{print $1}'`
setenv KDM `grep \'kdm blkdat.input | awk '{print $1}'`
setenv DP00 `grep \'dp00\ blkdat.input | awk '{print $1}'`
setenv DP00X `grep \'dp00x blkdat.input | awk '{print $1}'`
setenv DP00F `grep \'dp00f blkdat.input | awk '{print $1}'`
setenv DS00 `grep \'ds00\ blkdat.input | awk '{print $1}'`
setenv DS00X `grep \'ds00x blkdat.input | awk '{print $1}'`
setenv DS00F `grep \'ds00f blkdat.input | awk '{print $1}'`
setenv SIGMA `grep \'sigma blkdat.input | awk '{print $1}'`
setenv INIFLG `grep \'iniflg blkdat.input | awk '{print $1}'`
setenv JERLV0 `grep \'jerlv0 blkdat.input | awk '{print $1}'`
setenv BNSTFQ `grep \'bnstfq blkdat.input | awk '{print $1}'`
setenv NESTFQ `grep \'nestfq blkdat.input | awk '{print $1}'`
setenv VORTFQ `grep \'vortfq blkdat.input | awk '{print $1}'`
setenv VORTNO `grep \'vortno blkdat.input | awk '{print $1}'`
setenv BACLIN `grep \'baclin blkdat.input | awk '{print $1}'`
setenv BATROP `grep \'batrop blkdat.input | awk '{print $1}'`
setenv HYBFLG `grep \'hybflg blkdat.input | awk '{print $1}'`
setenv ADVFLG `grep \'advflg blkdat.input | awk '{print $1}'`
setenv SLIP `grep \'slip blkdat.input | awk '{print $1}'`
setenv VISCO2 `grep \'visco2 blkdat.input | awk '{print $1}'`
setenv VISCO4 `grep \'visco4 blkdat.input | awk '{print $1}'`
setenv VELDF2 `grep \'veldf2 blkdat.input | awk '{print $1}'`
setenv VELDF4 `grep \'veldf4 blkdat.input | awk '{print $1}'`
setenv THKDF2 `grep \'thkdf2 blkdat.input | awk '{print $1}'`
setenv THKDF4 `grep \'thkdf4 blkdat.input | awk '{print $1}'`
setenv TEMDF2 `grep \'temdf2 blkdat.input | awk '{print $1}'`
setenv VERTMX `grep \'vertmx blkdat.input | awk '{print $1}'`
setenv CBAR `grep \'cbar blkdat.input | awk '{print $1}'`
setenv CB `grep \'cb\ blkdat.input | awk '{print $1}'`
setenv THKBOT `grep \'thkbot blkdat.input | awk '{print $1}'`
setenv SIGJMP `grep \'sigjmp blkdat.input | awk '{print $1}'`
setenv TMLJMP `grep \'tmljmp blkdat.input | awk '{print $1}'`
setenv THKMLR `grep \'thkmlr blkdat.input | awk '{print $1}'`
setenv MLFLAG `grep \'mlflag blkdat.input | awk '{print $1}'`
setenv CLMFLG `grep \'clmflg blkdat.input | awk '{print $1}'`
setenv LBFLAG `grep \'lbflag blkdat.input | awk '{print $1}'`
setenv WNDFLG `grep \'wndflg blkdat.input | awk '{print $1}'`
setenv FLXFLG `grep \'flxflg blkdat.input | awk '{print $1}'`
setenv RELAX `grep \'relax blkdat.input | awk '{print $1}'`
setenv SRELAX `grep \'srelax blkdat.input | awk '{print $1}'`
setenv TRELAX `grep \'trelax blkdat.input | awk '{print $1}'`
setenv TRCRLX `grep \'trcrlx blkdat.input | awk '{print $1}'`
# addition informatin written to netcdf files:
setenv CDF_TITLE "HYCOM"
setenv CDF_INST "NOAA AOML"
# set some directory names:
#set RUNDIR=`mktemp -d $TMPDIR/tfile.XXXXXXXXXX`
#set ARCHV2NCDF2D=${HYCOMDIR}/ALL/archive/src/archv2ncdf2d
#set OUTPUTDIR=${HYCOMDIR}/${REGION}/expt_${IEXPT}/data/ncdf/
#cd ${RUNDIR}
#ln -s ${TOPODIR}/regional.grid.nc
#ln -s ${DEPTHDIR}/depth.nc regional.depth.nc
# Iterate over all arch.[ab] files in the directory
#touch rundirarchives
#if (-e ${HYCOMDIR}/${REGION}/expt_${IEXPT}/rundir && ${ARCH} != aster) then
# ls ${HYCOMDIR}/${REGION}/expt_${IEXPT}/rundir/archv*.nc > rundirarchives
#endif
#if (! -z rundirarchives) then
# echo 'using rundir'
# set INFILES=`ls ${HYCOMDIR}/${REGION}/expt_${IEXPT}/rundir/archv*.nc | sort `
#else
# echo 'using data'
# set INFILES=`ls ${HYCOMDIR}/${REGION}/expt_${IEXPT}/data/archv*.nc | sort `
#endif
#foreach INFILE ( ${INFILES} )
# set OUTFILE=./`basename $INFILE nc`nc
# setenv CDF051 ${OUTFILE}
setenv CDF051 dummy.nc
setenv CDF052 dummy_u.nc
/bin/rm $CDF051
/bin/rm $CDF052
#
# rm -f ${OUTFILE}
./archv2ncdf2d << EOF
dummy.a
netCDF
000 'iexpt ' = experiment number x10 (000=from archive file)
${YRF} 'yrflag' = days in year flag (0=360J16,1=366J16,2=366J01,3-actual)
${IDM} 'idm ' = longitudinal array size
${JDM} 'jdm ' = latitudinal array size
${KDM} 'kdm ' = number of layers
${THB} 'thbase' = reference density (sigma units)
0 'smooth' = smooth fields before plotting (0=F,1=T)
0 'mthin ' = mask thin layers from plots (0=F,1=T)
1 'iorign' = i-origin of plotted subregion
1 'jorign' = j-origin of plotted subregion
0 'idmp ' = i-extent of plotted subregion (<=idm; 0 implies idm)
0 'jdmp ' = j-extent of plotted subregion (<=jdm; 0 implies jdm)
51 'botio ' = bathymetry I/O unit (0 no I/O)
51 'flxio ' = surf. heat flux I/O unit (0 no I/O)
51 'empio ' = surf. evap-pcip I/O unit (0 no I/O)
51 'ttrio ' = surf. temp trend I/O unit (0 no I/O)
51 'strio ' = surf. saln trend I/O unit (0 no I/O)
0 'icvio ' = ice coverage I/O unit (0 no I/O)
0 'ithio ' = ice thickness I/O unit (0 no I/O)
0 'ictio ' = ice temperature I/O unit (0 no I/O)
51 'sshio ' = sea surf. height I/O unit (0 no I/O)
0 'guvio ' = sea surf. height I/O unit (0 no I/O)
0 'gvvio ' = sea surf. height I/O unit (0 no I/O)
0 'gspio ' = sea surf. height I/O unit (0 no I/O)
51 'buvio ' = baro. u. velocity I/O unit (0 no I/O)
51 'bvvio ' = baro. v. velocity I/O unit (0 no I/O)
51 'bspio ' = bar. speed I/O unit (0 no I/O)
51 'bsfio ' = baro. strmfn. I/O unit (0 no I/O)
51 'uvmio ' = mix. lay. u-vel. I/O unit (0 no I/O)
51 'vvmio ' = mix. lay. v-vel. I/O unit (0 no I/O)
51 'stxio ' = stress u-vel. I/O unit (0 no I/O)
51 'styio ' = stress y-vel. I/O unit (0 no I/O)
51 'spmio ' = mix. lay. speed I/O unit (0 no I/O)
51 'bltio ' = bnd. lay. thick. I/O unit (0 no I/O)
51 'mltio ' = mix. lay. thick. I/O unit (0 no I/O)
51 'sstio ' = mix. lay. temp. I/O unit (0 no I/O)
51 'sssio ' = mix. lay. saln. I/O unit (0 no I/O)
51 'ssdio ' = mix. lay. dens. I/O unit (0 no I/O)
1 'kf ' = first output layer (=0 end output; <0 label with layer #)
${KDM} 'kl ' = last output layer
52 'uvlio ' = layer k u-vel. I/O unit (0 no I/O)
52 'vvlio ' = layer k v-vel. I/O unit (0 no I/O)
0 'splio ' = layer k speed. I/O unit (0 no I/O)
0 'wvlio ' = layer k w.vel. I/O unit (0 no I/O)
0 'infio ' = layer k i.dep. I/O unit (0 no I/O)
52 'thkio ' = layer k thick. I/O unit (0 no I/O)
52 'temio ' = layer k temp I/O unit (0 no I/O)
52 'salio ' = layer k saln. I/O unit (0 no I/O)
0 'tthio ' = layer k dens, I/O unit (0 no I/O)
0 'sfnio ' = layer k strmfn. I/O unit (0 no I/O)
0 'kf ' = first output layer (=0 end output; <0 label with layer #)
EOF
#end
# The ncrcat utility is from the nco projects. It concatenates the files produced above
#mkdir -p ${OUTPUTDIR}
#rm -f ${OUTPUTDIR}/archv.${REGION}.${IEXPT}.nc
#ls archv*.nc | sort | ncrcat ${OUTPUTDIR}/archv.${REGION}.${IEXPT}.nc
# clean up:
#rm -rf ${RUNDIR}