I've used below code from this reference : https://stackoverflow.com/a/2288181/4819200
<?php
//http://domain.com/script/script.php?username=username&passwd=password
define( '_JEXEC', 1 );
define('JPATH_BASE', '../' );
define( 'DS', DIRECTORY_SEPARATOR );
require_once('../configuration.php');
require_once ( JPATH_BASE .DS.'includes'.DS.'defines.php' );
require_once ( JPATH_BASE .DS.'includes'.DS.'framework.php' );
require_once ( JPATH_BASE .DS.'libraries'.DS.'joomla'.DS.'factory.php' );
/* Create the Application */
$mainframe =& JFactory::getApplication('site');
jimport('joomla.plugin.helper');
$credentials = array();
$credentials['username'] = JRequest::getVar('username', '', 'method', 'username');
$credentials['password'] = JRequest::getVar('passwd', '', 'method', 'passwd');
//perform the login action
$error = $mainframe->login($credentials);
$user = JFactory::getUser();
//now you are logged in
$mainframe->logout();
//now you are logged out
Now, the Issue
It was working in Joomla 2.3 version and it stopped working in 3.4 version. Now, it is not returning from line $mainframe =& JFactory::getApplication('site');.
You can suggest me code for latest version.
Note : I'm not joomla guy. But, I've worked on some PHP frameworks.
In Joomla 3 you can use this code to get User Object from outside Joomla
<?php
//http://domain.com/script/script.php?username=username&passwd=password
$dir = '/var/www/joomla'; // path to your joomla installation directory
define( '_JEXEC', 1 );
define( 'JPATH_BASE', $dir);
define( 'DS', '/' );
require_once ( JPATH_BASE .DS . 'configuration.php' );
require_once ( JPATH_BASE .DS.'includes'.DS.'defines.php' );
require_once ( JPATH_BASE .DS.'includes'.DS.'framework.php' );
require_once ( JPATH_BASE .DS.'libraries'.DS.'joomla'.DS.'factory.php' );
//Then you can call the classes this way
$mainframe = JFactory::getApplication('site');
/* Create the Application */
//$mainframe =& JFactory::getApplication('site');
jimport('joomla.plugin.helper');
$credentials = array();
$credentials['username'] = JRequest::getVar('username', '', 'method', 'username');
$credentials['password'] = JRequest::getVar('passwd', '', 'method', 'passwd');
//perform the login action
$error = $mainframe->login($credentials);
$user = JFactory::getUser();
//now you are logged in
$mainframe->logout();