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. 

protected:
    Chunk generate() override;
private:
    const size_t block_size;
    const NamesAndTypesList columns;
    const StorageLog & storage;
    const size_t rows_limit;      
    size_t rows_read = 0;
    bool is_finished = false;
    const std::vector<size_t> offsets;
    const std::vector<size_t> file_sizes;
    const bool limited_by_file_sizes;
    const ReadSettings read_settings;
    struct Stream
    {
        Stream(const DiskPtr & disk, const String & data_path, size_t offset, size_t file_size, bool limited_by_file_size, ReadSettings read_settings_)