Make GATPFit working directory if it doesn't exist when you need it.

This helps things like the Abraham data estimator class, which don't do
the proper startup required to make the directory.
Print warning instead of crashing weirdly if trying to read from Tree before it's loaded.

It used to give a bizarre "TreeNode can't be cast into HierarchyTreeNode" type of crash,
because the blank HierarchyTree would have a root element that's a TreeNode (from the parent
constructor). Perhaps this should be an exception not a warning, but at least it now tells
you the problem which may help debugging.
Fix the Abraham class for generating stand-alone Abraham parameter estimates.

The Abraham group definitions weren't being loaded. Now they should be.
Abraham class now outputs the Abraham parameters, not the logK
Added example input and shell script for AbrahamDataEstimator

This stand-alone script generates estimates of Abraham parameters.
Currently undocumented, but the example should help.
Updates to the Abraham group estimation groups database from ajalan/autoxidation_rebased

This is all Amrit's (@ajalan) updates to the Abraham groups Dictionary/Library/Tree
currently on his autoxidation_rebased branch. This should bring the master up to date
in this regard. (Although there are other changes on that branch that should also be merged).
I believe some of the changes fix 1,2-diols. I'm not sure about the others.
Added a few more solutes to the example AbrahamDataEstimator input file.
Merge in Abraham data estimator fixes.

Some changes to the stand-alone class for estimating Abraham parameters,
an example input file and shell script to run it,
and some changes to the group definitions and library values taken from
Amrit's autoxidation_rebased branch. Overall, this should now reproduce
the data reported in http://dx.doi.org/10.1021/jp310824h
Fix bug in estimation of Enthalpy of solvation.

It seems we were using the Abraham parameters instead of the Mintz parameters.
i.e. we were using logK (unitless) in place of deltaH (kJ/mol)

On @ajalan's autoxidation_rebased branch it looks like this got fixed in the commit
8ec4e24e8fbc663d1f03c421345b6678552a2e24. Until his branch is merged in, this
fix will suffice.
Fix typos, inaccuracies, etc. in GATP_Solvation.

Adding some significant figures to constants,
correcting the units in the comments, and removing
a few typing mistakes.
Add comments to transport estimator libraries to label columns.

It's not obvious what these numbers mean. I believe this to be right.
(or at least that's what the variables are named that are used to read these files!)
Added rmg.mit.edu link to homepage, on Bill's request
Remove hardcoding of max reactant/product numbers from JDAS.

Everybody ought to use Structure.MAX_REACTANT_NUMBER and
Structure.MAX_PRODUCT_NUMBER as much as possible. This is only a small step
toward making it easier to change the maximum reactant and product numbers.
Increment maximum product count from 3 to 4 in RMG.

This allows us to handle more non-elementary reactions in seed mechanisms
and reaction libraries. Whether we ought to be using such reactions is
another matter, but at least we now have the capability.
Updated DASSL to handle up to four products in reactions.

The reaction arrays for regular, third body, Lindemann, and Troe reactions
needed to be updated to include another element for the new product. (Aside:
why aren't these arrays two-dimensional?)

DASPK has not yet been updated, since it would be even more involved, and
I'm not set up to test it at the moment. However, the sorts of changes made
here should be similar to changes that would be needed there.

Note that the maximum number of reactants and products is still hardcoded in
many places.
Updated DASPK to handle up to four products in reactions.

The changes mirror those recently made to DASSL, although these have not yet
been tested. Also, there is way too much duplicate code in both our DASSL
and DASPK implementations.