Automatically set permalink structure when theme is activated.

wp-options-permalink-set.php

add_action('after_switch_theme', 'mytheme_install');
function mytheme_install() {
  //Sets permalink Structure
	$wp_rewrite->set_permalink_structure( '/%year%/%monthnum%/%day%/%postname%/' );
	//Update rewrite rules, sets our custom rules
	flush_rewrite_rules();
}