To run the command, you just need to enter 'windchill wt.auth.Authentication' in a Windchill shell (without the quotes). This will pop up a dialog box prompting you to enter a username and password for authentication. If you're running a headless environment, you can pass the username/password on the command line by running the below command instead:
windchill --javaargs="-Dcom.ptc.net.auth.user=<username> -Dcom.ptc.net.auth.password=<password>" wt.auth.Authentication
Replacing <username> and <password> with a valid username and password.