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. 

{
    for (const auto & data_file : data_files)
        file_checker.update(data_file.path);
    if (use_marks_file)
        file_checker.update(marks_file_path);
    file_checker.save();
    total_bytes = file_checker.getTotalSize();
}
void StorageLog::rename(const String & new_path_to_table_data, const StorageID & new_table_id)
{
    assert(table_path != new_path_to_table_data);
    {
        disk->moveDirectory(table_path, new_path_to_table_data);
        table_path = new_path_to_table_data;
        file_checker.setPath(table_path + "sizes.json");
        for (auto & data_file : data_files)
            data_file.path = table_path + fileName(data_file.path);
        marks_file_path = table_path + DBMS_STORAGE_LOG_MARKS_FILE_NAME;
    }
    renameInMemory(new_table_id);
}
static std::chrono::seconds getLockTimeout(ContextPtr context)
{
    const Settings & settings = 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};
}
void StorageLog::truncate(const ASTPtr &, const StorageMetadataPtr &, ContextPtr local_context, TableExclusiveLockHolder &)