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 String & zookeeper_path_,
    const String & replica_name_,
    bool attach,
    const StorageID & table_id_,
    const String & relative_data_path_,
    const StorageInMemoryMetadata & metadata_,
    ContextMutablePtr context_,
    const String & date_column_name,
    const MergingParams & merging_params_,
    std::unique_ptr<MergeTreeSettings> settings_,
    bool has_force_restore_data_flag,
    RenamingRestrictions renaming_restrictions_)
    : MergeTreeData(table_id_,
                    relative_data_path_,
                    metadata_,
                    context_,
                    date_column_name,
                    merging_params_,
                    std::move(settings_),
                    true,                   
                    attach,
                    [this] (const std::string & name) { enqueuePartForCheck(name); })
    , zookeeper_name(zkutil::extractZooKeeperName(zookeeper_path_))
    , zookeeper_path(zkutil::extractZooKeeperPath(zookeeper_path_,  !attach, log))
    , replica_name(replica_name_)
    , replica_path(fs::path(zookeeper_path) / "replicas" / replica_name_)
    , reader(*this)
    , writer(*this)
    , merger_mutator(*this, getContext()->getMergeMutateExecutor()->getMaxTasksCount())
    , merge_strategy_picker(*this)