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. 

const StorageStripeLog & storage_,
        const StorageSnapshotPtr & storage_snapshot_,
        const Names & column_names,
        ReadSettings read_settings_,
        std::shared_ptr<const IndexForNativeFormat> indices_,
        IndexForNativeFormat::Blocks::const_iterator index_begin_,
        IndexForNativeFormat::Blocks::const_iterator index_end_,
        size_t file_size_)
        : ISource(getHeader(storage_snapshot_, column_names, index_begin_, index_end_))
        , storage(storage_)
        , storage_snapshot(storage_snapshot_)
        , read_settings(std::move(read_settings_))
        , indices(indices_)
        , index_begin(index_begin_)
        , index_end(index_end_)
        , file_size(file_size_)
    {
    }
    String getName() const override { return "StripeLog"; }