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. 

dest_table_storage->renameTempPartAndReplaceUnlocked(part, transaction, builder, dest_data_parts_lock);
                }
                for (size_t i = 0; i < dst_parts.size(); ++i)
                    dest_table_storage->lockSharedData(*dst_parts[i], false, hardlinked_files_for_parts[i]);
                Coordination::Error code = zookeeper->tryMulti(ops, op_results);
                if (code == Coordination::Error::ZBADVERSION)
                    continue;
                else
                    zkutil::KeeperMultiException::check(code, ops, op_results);
                parts_to_remove = removePartsInRangeFromWorkingSetAndGetPartsToRemoveFromZooKeeper(NO_TRANSACTION_RAW, drop_range, src_data_parts_lock);
                transaction.commit(&src_data_parts_lock);
            }
            PartLog::addNewParts(getContext(), dst_parts, watch.elapsed());
        }
        catch (...)
        {
            PartLog::addNewParts(getContext(), dst_parts, watch.elapsed(), ExecutionStatus::fromCurrentException());
            for (const auto & dst_part : dst_parts)
                dest_table_storage->unlockSharedData(*dst_part);
            throw;
        }
        String log_znode_path = dynamic_cast<const Coordination::CreateResponse &>(*op_results.back()).path_created;
        entry.znode_name = log_znode_path.substr(log_znode_path.find_last_of('/') + 1);
        for (auto & lock : ephemeral_locks)
            lock.assumeUnlocked();
        removePartsFromZooKeeperWithRetries(parts_to_remove);
        parts_to_remove.clear();
        cleanup_thread.wakeup();
        lock2.reset();
        dest_table_storage->waitForLogEntryToBeProcessedIfNecessary(entry, query_context);