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 Settings & settings = local_context->getSettingsRef();
    Int64 lock_timeout = settings.lock_acquire_timeout.totalSeconds();
    if (settings.max_execution_time.totalSeconds() != 0 && settings.max_execution_time.totalSeconds() < lock_timeout)
        lock_timeout = settings.max_execution_time.totalSeconds();
    return std::chrono::seconds{lock_timeout};
}
Pipe StorageStripeLog::read(
    const Names & column_names,
    const StorageSnapshotPtr & storage_snapshot,
    SelectQueryInfo & ,
    ContextPtr local_context,
    QueryProcessingStage::Enum ,
    const size_t ,
    unsigned num_streams)
{
    storage_snapshot->check(column_names);
    auto lock_timeout = getLockTimeout(local_context);
    loadIndices(lock_timeout);
    ReadLock lock{rwlock, lock_timeout};
    if (!lock)
        throw Exception("Lock timeout exceeded", ErrorCodes::TIMEOUT_EXCEEDED);