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. 

local_context->getSettingsRef().max_parser_depth);
    applyMetadataChangesToCreateQuery(ast, metadata);
    statement = getObjectDefinitionFromCreateQuery(ast);
    {
        WriteBufferFromFile out(table_metadata_tmp_path, statement.size(), O_WRONLY | O_CREAT | O_EXCL);
        writeString(statement, out);
        out.next();
        if (local_context->getSettingsRef().fsync_metadata)
            out.sync();
        out.close();
    }
    TableNamesSet new_dependencies = getDependenciesSetFromCreateQuery(local_context->getGlobalContext(), table_id.getQualifiedName(), ast);
    DatabaseCatalog::instance().updateLoadingDependencies(table_id, std::move(new_dependencies));
    commitAlterTable(table_id, table_metadata_tmp_path, table_metadata_path, statement, local_context);
}
void DatabaseOrdinary::commitAlterTable(const StorageID &, const String & table_metadata_tmp_path, const String & table_metadata_path, const String & , ContextPtr )
{
    try
    {
        
        fs::rename(table_metadata_tmp_path, table_metadata_path);
    }
    catch (...)
    {
        fs::remove(table_metadata_tmp_path);
        throw;
    }
}
}