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. 

{
    WriteLock lock{rwlock, getLockTimeout(local_context)};
    if (!lock)
        throw Exception("Lock timeout exceeded", ErrorCodes::TIMEOUT_EXCEEDED);
    disk->clearDirectory(table_path);
    for (auto & data_file : data_files)
    {
        data_file.marks.clear();
        file_checker.setEmpty(data_file.path);
    }
    if (use_marks_file)
        file_checker.setEmpty(marks_file_path);
    marks_loaded = true;
    num_marks_saved = 0;
    getContext()->dropMMappedFileCache();
}
Pipe StorageLog::read(
    const Names & column_names,
    const StorageSnapshotPtr & storage_snapshot,
    SelectQueryInfo & ,
    ContextPtr local_context,
    QueryProcessingStage::Enum ,
    size_t max_block_size,
    unsigned num_streams)
{
    storage_snapshot->check(column_names);