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. 

DiskPtr disk_,
    const String & relative_path_,
    const StorageID & table_id_,
    const ColumnsDescription & columns_,
    const ConstraintsDescription & constraints_,
    const String & comment,
    bool attach,
    ContextMutablePtr context_)
    : IStorage(table_id_)
    , WithMutableContext(context_)
    , disk(std::move(disk_))
    , table_path(relative_path_)
    , data_file_path(table_path + "data.bin")
    , index_file_path(table_path + "index.mrk")
    , file_checker(disk, table_path + "sizes.json")
    , max_compress_block_size(context_->getSettings().max_compress_block_size)
    , log(&Poco::Logger::get("StorageStripeLog"))
{
    StorageInMemoryMetadata storage_metadata;
    storage_metadata.setColumns(columns_);