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. 

{
    ThreadPool pool;
    DatabaseCatalog::instance().getSystemDatabase()->startupTables(pool, LoadingStrictnessLevel::FORCE_RESTORE);
}
void loadMetadataSystem(ContextMutablePtr context)
{
    loadSystemDatabaseImpl(context, DatabaseCatalog::SYSTEM_DATABASE, "Atomic");
    loadSystemDatabaseImpl(context, DatabaseCatalog::INFORMATION_SCHEMA, "Memory");
    loadSystemDatabaseImpl(context, DatabaseCatalog::INFORMATION_SCHEMA_UPPERCASE, "Memory");
    TablesLoader::Databases databases =
    {
        {DatabaseCatalog::SYSTEM_DATABASE, DatabaseCatalog::instance().getSystemDatabase()},
        {DatabaseCatalog::INFORMATION_SCHEMA, DatabaseCatalog::instance().getDatabase(DatabaseCatalog::INFORMATION_SCHEMA)},
        {DatabaseCatalog::INFORMATION_SCHEMA_UPPERCASE, DatabaseCatalog::instance().getDatabase(DatabaseCatalog::INFORMATION_SCHEMA_UPPERCASE)},
    };
    TablesLoader loader{context, databases, LoadingStrictnessLevel::FORCE_RESTORE};
    loader.loadTables();
    
}
}