batch_runs.sh

#!/bin/bash

# ARRAY1=(5. 10. 20. 30. 40. 50. 60. 70. 80. 90. 100. 125. 150. 175. 200. 250. 300. 350.) # peak jet
# ARRAY2=(0. 0.1 0.2 1.) # cvis in Smagorinsky model

ARRAY1=(50. 100. 150. ) # peak jet
ARRAY2=(0. 0.1 0.2 1.) # cvis in Smagorinsky model


ELEMENTS1=${#ARRAY1[@]} # elements in first array
ELEMENTS2=${#ARRAY2[@]} # elements in second array

mkdir /tmp/${USER}

for (( i=0;i<$ELEMENTS1;i++)); do
	for (( j=0;j<$ELEMENTS2;j++)); do
			# Runs with the hm process switched on:
	 		echo ${ARRAY1[${i}]} ${ARRAY2[${j}]} 
            sed -e "s|output.nc|${USER}/output_${i}_${j}.nc|" namelist.in > namelist.tmp
			sed -e "s/u_jet=50./u_jet=${ARRAY1[${i}]}/" namelist.tmp > /tmp/namelist.tmp2
 			sed -e "s/cvis=0.2/cvis=${ARRAY2[${j}]}/" /tmp/namelist.tmp2 > namelist.run
 			
 			
 			
            if [ -z "$1" ]
            then
                    mpiexec -n 1 ./main.exe namelist.run > /tmp/${USER}/std.out
            else
                    mpiexec -n $1 ./main.exe namelist.run > /tmp/${USER}/std.out
            fi
            rm namelist.tmp 
            rm namelist.tmp2

 			
	done
done