Mixing in Northern North Sea including the NPZD bio-geochemical model: http://www.gotm.net/index.php?go=software&page=testcases
More about this case: http://www.gotm.net/pages/documentation/manual/stable/html/node237.html#nns_annual
Biogeochemical Model: NPZD (4 variables)
Advection scheme for vertical motion: TVD with ULTIMATE QUICKEST
ODE scheme for source and sink dynamics: Modified Patankar-RK (2. order, conservat., posit.)
bio_npzd.nml
I am going to play around with this file.
".value" files
This type of file gives you the list of parameters or T/F statements of your choice for the run. Can be useful to keep track of your simulation settings.
sst and sss restoring (every 3 hours with 3-D model output)
temperature and salinity resotring (whole depth, every 12 hours with 3-D model output)
dt = 1 hour
Sensitivity Analysis: Select 5 parameters.
Parameter Number. Code Name: Default Value: Line Number in "bio_npzd.nml"
- I_min: 25.: L39
- rmax: 1.: L40
- gmax: 0.2: L41
- alpha: 1.35: L43
- rzd: 0.02: L49
How to rewrite a specific line using sed: http://www.linuxquestions.org/questions/programming-9/bash-replace-a-line-in-text-file-631208/#post3102926
c=1 for -5%
c=2 for +5%
c=3 for -25%
c=4 for +25%
I created a simpler script than the one I created before for PISCES:
sensitivity.sh
#---------------------------------------------------------------
for it in `seq 1 5`; #Number of cases
do
for it2 in `seq 1 4`; #Number of parameters
do
testname="p${it}c${it2}.nc" #p=parameter number, c=case number
casenum=${testname:3:1}
if [ $casenum -eq 1 ]
then
variation="0.8"
elif [ $casenum -eq 2 ]
then
variation="0.95"
elif [ $casenum -eq 3 ]
then
variation="1.05"
elif [ $casenum -eq 4 ]
then
variation="1.2"
fi
parnum=${testname:1:1}
if [ $parnum -eq 1 ]
then
sed -i "39s/.*/ I_min= `echo "scale=5;25.*$variation"|bc`/" bio_npzd.nml
grep "I_min=" bio_npzd.nml >> samemo.txt
elif [ $parnum -eq 2 ]
then
sed -i "40s/.*/ rmax= `echo "scale=5;1.*$variation"|bc`/" bio_npzd.nml
grep "rmax=" bio_npzd.nml >> samemo.txt
elif [ $parnum -eq 3 ]
then
sed -i "41s/.*/ gmax= `echo "scale=5;0.2*$variation"|bc`/" bio_npzd.nml
grep "gmax=" bio_npzd.nml >> samemo.txt
elif [ $parnum -eq 4 ]
then
sed -i "43s/.*/ alpha= `echo "scale=5;1.35*$variation"|bc`/" bio_npzd.nml
grep "alpha=" bio_npzd.nml >> samemo.txt
elif [ $parnum -eq 5 ]
then
sed -i "49s/.*/ rzd= `echo "scale=5;0.02*$variation"|bc`/" bio_npzd.nml
grep "rzd=" bio_npzd.nml >> samemo.txt
fi
./rungotm
mv nns_annual.nc output/$testname
cp bio_npzd_original.nml bio_npzd.nml
done
done
#------------------------------------------------------
By producing output for each run in "samemo.txt", it helped me to check if the modifications were made in "bio_npzd.nml" appropriately.
One thing I learned from making this script: the square brackets [ ] in IF statements have to be isolated (a space before and after [ or ]).
