import java.io.FileReader;
import java.util.LinkedList;
import java.util.Scanner;

public class Pr1002 {

    public static void main(String[] args) {
        LinkedList<Long> listOfNum = new LinkedList<Long>();
        try {

            Scanner sc = new Scanner(new FileReader(args[0]));
            while (sc.hasNext()) {
                listOfNum.addFirst(sc.nextLong());
            }
            while (!listOfNum.isEmpty()) {
                System.out.printf("%.4f", Math.sqrt(listOfNum.removeFirst()));
                System.out.println();
            }

        } catch (Exception e) {
            System.out.println(e.getMessage());
        }

    }
}

>> Scanner sc = new Scanner(new FileReader(args[0]));
I think you're to assume all input comes from 'System.in' and not be specify as a program argument, so 'java myprogram inputfile.txt shouldn't work'.