wp_enqueue script

custom.js

(function($) {
	
	// $ Works! You can test it with next line if you like
	 console.log("I'm alive!");
	
})( jQuery );

functions.php

//Just the script
wp_enqueue_script(
		'custom',
		get_stylesheet_directory_uri() . '/js/custom.js',
		array('jquery'),
		null,
		true
	 );

//The entire function
//Function includes deregistering the default jquery
// include custom jQuery

function shapeSpace_include_custom_jquery() {
	wp_deregister_script('jquery');
	wp_enqueue_script(
		'jquery',
		'https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js',
		array(),
		null,
		true);

}
add_action('wp_enqueue_scripts', 'shapeSpace_include_custom_jquery');