Atom types are now case sensitive.

This must be done in order to allow both the Cs (carbon with only single
bonds) and CS (carbon with double bond to sulfur) atom types to coexist.
Without this, using group additivity or rate rules to estimate parameters
could lead to incorrect leaves in the tree due to the mistaking of CS for
Cs.

Closes #284.
Added date stamp of RMG job to chemkin file.
Incorrect case usage in DASPK Makefile fix.

Remember that Makefiles are case-sensitive...
Typo in kinetics database for cyclic ether formation.
Update copyright in license to 2013.
Update documentation version references to 4.0 for the new release.
Update RMG credits to include new developers.
Updated documentation example condition files page to include sulfur
and liquid oxidation examples.
Added `Tips for Setting up a RMG Job` page to documentation.
Removed deprecated Sulfur database.
Revised `Tips for Setting up an RMG Job.`
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.
Adjusted A factor in H_Abstraction rule #75.

The previous A-factor was orders of magnitude larger than other A-factors
from the Saeys rules. We attempted to use the Saeys group values to
estimate the correct value, and got a number far closer to 3e12 than
3e18. This is also much more consistent with an estimate from Tsang (in
the NIST database).
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