refined the script

mcluster_script.sh

 #!/bin/bash
+
+#####
+# Script to execute mcluster to set up inital settings for a cluster.
+# Useage: run the script. Change the values of NAME_RUN, MCLUSTER_COMMANDS and TARGET_DIR to your liking. After running this script you can use the output to feed it to nbody6
+######
+
 # TODO:
-# rename the files
 # Check if dir exists.
 
+# Dont change these settings
 MCLUSTER_CONFIG_DIR='/vol/ph/astro_code/dhendriks/work_dir/mcluster'
 MCLUSTER_EXECUTABLE='/vol/ph/astro_code/dhendriks/mcluster/mcluster'
-NAME_RUN='test'
 
+
+# Change these settings
+TARGET_DIR=$MCLUSTER_CONFIG_DIR
+NAME_RUN='test'
 # Store settings for mcluster in here.
 MCLUSTER_COMMANDS="-C0 -o"
 
 
+# Check if dir is empty: if not: empty it
+DIR="test"
+if [ "$(ls -A $TARGET_DIR)" ]; then
+     echo "Take action $TARGET_DIR is not Empty"
+    echo "Deleting content:"
+    rm $TARGET_DIR/*
+else
+    echo "$TARGET_DIR is Empty"
+fi
+
+# Execute mcluster cmd
 $MCLUSTER_EXECUTABLE $MCLUSTER_COMMANDS $MCLUSTER_CONFIG_DIR/$NAME_RUN | tee $MCLUSTER_CONFIG_DIR/$NAME_RUN.summary
 
 # Write command to file