Families.txt should be in working dir rather than RMG folder

[nickvandewiele]

Rather a feature request than an issue:

The families.txt file with the activated reaction families should be part of the working directory rather than the RMG folder. In this way, multiple copies of families.txt can exist in parallel.

If a RMG job is submitted to the scheduler, and still in the waiting list, rather than being executed immediately, the user cannot submit new jobs, because families.txt is still not read-in by the 'waiting' RMG simulation.

Based on a true story.

[ajalan]

Please look at a potential solution in this commit 937d3696

The burden of making sure that all jobs have been submitted before the current families.txt file is loaded still falls on the user but this is a start.

[jwallen]

I don't like the idea of having to write files to the installation directory for individual jobs; it's messy and error-prone. I'd say the best approach is to add the ability to turn on/off families in the condition file itself (like you can do with seed mechanisms and reaction libraries).

An easier-to-implement alternative would be to have RMG check the job directory for families.txt and read that over the one in the kinetics_groups folder if present.

[ajalan]

I agree. As I said, this is a start and not something we would recommend to external users. Ideally, we would like to not touch the installation directory at all. Continuing with what @jwallen suggested, we could add a keyword to the condition file saying "Reaction Families: default/read" where "default" reads in the families.txt file in the installation directory and "read" uses the one in the job directory.