GreenGroup/RMG-Java — pull request #279 by rwest (2012-11-27 00:34:20+00:00)
Title: Finer control over various paths via environment variables.

The idea here is that you can control where things go, where is used as scratch, etc. etc. via environment variables. This would offer flexibility for running on clusters: you set up your queue job script to define the variables, and can then, for example, share your QM folders across jobs, and use local scratch drives for temporary files, etc.

So far, only these have been moved (and the defaults are such that they in fact stay where they were):

* `InChI` has been moved to `$RMG_JOB_SCRATCH/InChI`
* `$RMG/databases` has been moved to `$RMG_DATABASES`

I think Fame and Frankie, and perhaps the ODE solvers, could be made to use the $RMG_JOB_SCRATCH direcory, a bit like InChI.
It would be good to perhaps have an `$RMG_QM_FILES` variable for finished mopac jobs, although whether we also want a separate scratch for QM I'm not sure. The way QMLibrary is set up concurrent writes are impossible, so they have to be job-specific files. Thoughts?

Also, I have not tested all the other stand-alone classes besides RMG (eg. ThermoDataEstimator, etc.) but I tried not to break them.

It's not yet complete, so I'm not suggesting an immediate merge, but I think it runs correctly already.
If you want to build on this branch, or make comments below, please do so... (@keceli ?)
I'm running out of time this week.