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. 

{
        if (!server.isStopping())
            return false;
        size_t current_connections = server.currentConnections();
        LOG_DEBUG(log, "Server {}{}: {} ({} connections)",
            server.getDescription(),
            prefix,
            !current_connections ? "finished" : "waiting",
            current_connections);
        return !current_connections;
    };
    std::erase_if(servers, std::bind_front(check_server, " (from one of previous reload)"));
    for (auto & server : servers)
    {
        if (!server.isStopping())
        {
            bool has_host = std::find(listen_hosts.begin(), listen_hosts.end(), server.getListenHost()) != listen_hosts.end();
            bool has_port = !config.getString(server.getPortName(), "").empty();
            if (!has_host || !has_port || config.getInt(server.getPortName()) != server.portNumber())
            {
                server.stop();
                LOG_INFO(log, "Stopped listening for {}", server.getDescription());
            }
        }
    }
    createServers(config, listen_hosts, interserver_listen_hosts, listen_try, server_pool, async_metrics, servers,  true);
    std::erase_if(servers, std::bind_front(check_server, ""));
}
}