updated batch script

batch_runs.sh

@@ -1,21 +1,33 @@
-#! /bin/bash
+#!/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
 
 
 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/u_jet=50./u_jet=${ARRAY1[${i}]}/" namelist.in > /tmp/namelist.tmp
- 			sed -e "s/cvis=0.2/cvis=${ARRAY2[${j}]}/" /tmp/namelist.tmp > namelist.run
+            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
+
 
- 			#mpiexec -n 64 ./main.exe namelist.run > std.out
-
- 			#mv /tmp/output.nc /tmp/output_${i}_${j}.nc 		 			
+
+            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