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. 

StorageLog::StorageLog(
    const String & engine_name_,
    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_)
    , engine_name(engine_name_)
    , disk(std::move(disk_))
    , table_path(relative_path_)
    , use_marks_file(engine_name == "Log")
    , marks_file_path(table_path + DBMS_STORAGE_LOG_MARKS_FILE_NAME)
    , file_checker(disk, table_path + "sizes.json")
    , max_compress_block_size(context_->getSettingsRef().max_compress_block_size)
{
    StorageInMemoryMetadata storage_metadata;
    storage_metadata.setColumns(columns_);
    storage_metadata.setConstraints(constraints_);
    storage_metadata.setComment(comment);
    setInMemoryMetadata(storage_metadata);
    if (relative_path_.empty())
        throw Exception("Storage " + getName() + " requires data path", ErrorCodes::INCORRECT_FILE_NAME);