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. 

new_volume,
        relative_data_path,
        TMP_PREFIX + lost_part_name);
    DataPartStorageBuilderPtr data_part_storage_builder = std::make_shared<DataPartStorageBuilderOnDisk>(
        new_volume,
        relative_data_path,
        TMP_PREFIX + lost_part_name);
    auto new_data_part = createPart(
        lost_part_name,
        choosePartType(0, block.rows()),
        new_part_info,
        data_part_storage);
    if (settings->assign_part_uuids)
        new_data_part->uuid = UUIDHelpers::generateV4();
    new_data_part->setColumns(columns, {});
    new_data_part->rows_count = block.rows();
    {
        auto lock = lockParts();
        auto parts_in_partition = getDataPartsPartitionRange(new_part_info.partition_id);
        if (!parts_in_partition.empty())
        {
            new_data_part->partition = (*parts_in_partition.begin())->partition;
        }
        else if (auto parsed_partition = MergeTreePartition::tryParseValueFromID(
                     new_part_info.partition_id,
                     metadata_snapshot->getPartitionKey().sample_block))
        {
            new_data_part->partition = MergeTreePartition(*parsed_partition);
        }
        else