Make some adjustements in the README and usage string

Because the --atom option can take a variable number of arguments the
use of positional argument is made painfull. This commit introduce some
adjustements in the README and the usage string to take that into
account. Some adjustment were introduced in the previous commit as well
Mentions when the input is read from stdin

An error in position of the command line arguments can easily lead to
the program reading stdin when it is not expetcted; such behavior can
result in the user waiting forever. Now the program explicitely mention
that it will read stdin.