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 auto part_info = MergeTreePartInfo::tryParsePartName(it->name(), format_version);
            if (!part_info || part_info->partition_id != actual_part_info.partition_id)
                continue;
            const String part_old_name = part_info->getPartName();
            const VolumePtr volume = std::make_shared<SingleDiskVolume>("volume_" + part_old_name, disk);
            auto data_part_storage = std::make_shared<DataPartStorageOnDisk>(
                volume,
                fs::path(relative_data_path) / "detached",
                part_old_name);
            
            MergeTreeData::MutableDataPartPtr part = createPart(part_new_name, actual_part_info, data_part_storage);
            try
            {
                part->loadColumnsChecksumsIndexes(true, true);
            }
            catch (const Exception&)
            {
                
                
                continue;
            }
            if (entry.part_checksum == part->checksums.getTotalChecksumHex())
            {
                part->modification_time = data_part_storage->getLastModified().epochTime();
                return part;
            }
        }
    return {};
}
bool StorageReplicatedMergeTree::executeLogEntry(LogEntry & entry)