Ordinary database engine is deprecated but there is no simple mean to change database engine to Atomic for existing databases.

Possible options:
- ALTER DATABASE MODIFY ENGINE query.
- Flag that triggers migration at ClickHouse startup.

The latter should be easier to implement. 

catch (...)
    {
        tryLogCurrentException(log, "Caught exception while loading user defined objects");
        throw;
    }
    LOG_DEBUG(log, "Loaded user defined objects");
    LOG_INFO(log, "Loading metadata from {}", path_str);
    try
    {
        auto & database_catalog = DatabaseCatalog::instance();
        
        database_catalog.initializeAndLoadTemporaryDatabase();
        loadMetadataSystem(global_context);
        maybeConvertOrdinaryDatabaseToAtomic(global_context, DatabaseCatalog::instance().getSystemDatabase());
        
        global_context->initializeSystemLogs();
        global_context->setSystemZooKeeperLogAfterInitializationIfNeeded();
        
        attachSystemTablesServer(global_context, *database_catalog.getSystemDatabase(), has_zookeeper);
        attachInformationSchema(global_context, *database_catalog.getDatabase(DatabaseCatalog::INFORMATION_SCHEMA));
        attachInformationSchema(global_context, *database_catalog.getDatabase(DatabaseCatalog::INFORMATION_SCHEMA_UPPERCASE));
        
        
        
        database_catalog.loadMarkedAsDroppedTables();
        
        loadMetadata(global_context, default_database);
        startupSystemTables();
        database_catalog.loadDatabases();