Allow user inputted settings for generating flux diagram.
Merge branch 'master' of git://github.com/jwallen/RMG-Py
Fixed issue of too many edges in flux diagram for nondesired nodes.
Added atom and bond energy values for sulfur to CanTherm.

Now you can use CanTherm to compute thermo and kinetics for
sulfur-containing reactions! (Currently only for CBS-QB3.) Includes
spin-orbit coupling correction -- not needed for CBS-QB3, of course --
and a few bond energy corrections.
Also added sulfur handling to GaussianLog.loadGeometry().

This is so the correct atomic mass is used for the geometry, e.g. for
projecting hindered rotors.
Fewer calls to len() in updateUnimolecularReactionNetworks().

It's not actually the calls to len() that are causing this method to be
slow, but it's still better to not make billions of calls if they are not
required. This should not change the output at all.
Now storing pdep networks organized by source on CoreEdgeReactionModel.

This seems like a natural thing to do, since we do similar for species
and reactions already. It should make updateUnimolecularReactionNetworks()
go faster by reducing the network merging algorithm to O(N) from O(N^2).
Only iterate over updated networks when removing reverses from core..

Only the net reactions from the updated networks should have changed,
so there's no need to iterate over the entire list of core reactions.
Hopefully this speeds updateUnimolecularReactionNetworks() up some more.
Flux diagram creation extended focused on a centralized species

Flux diagrams can now be created that focus on a chosen species.
This is done by adding optional parameter centralSpecies to
-generateFluxDiagram
-createFluxDiagram

The parameter contains the name of the species mentioned in the chemkin
file.

If the parameter is passed to the method, then:
-the index of this particular species in speciesList is sought
-the "nodes" object is populated with the other reactants / products
in which the central species is mentioned
-creation of the edges object remains the same

The rest remains the same.
Merge remote-tracking branch 'origin/master' into fluxDiagram_Chosen_Species

Also, added declaration of global variables in methods for the global
variables like maximumNodeCount to avoid interpreting them as local
variables.
Merge remote-tracking branch 'josh/pdep'

This gives a three-fold speed up in the methylformate test case!
See issue #78 for details.
Added isIdenticalTo() and isSimilarTo() to ThermoModel class.

These methods assess the degree of similarity between two thermodynamics
models. Unlike the similar methods for the kinetics models, these do not
require the form of the models to be the same; instead, they simply
require that the models reproduce the same Cp, H, S, and G values over
a wide temperature range.
The diffModels tool now also compares the species thermo.

This seems like a logical feature, since we already compare the kinetics.
In particular, since some of the kinetic estimates depend on which
direction is exothermic, we would need to compare the thermo of the
species if the two models ever disagreed on the exothermic direction.

The compareModelSpecies() method was updated to return both matched
species in the list of common species, to better parallel the
compareModelReactions() method. The implementation of the former was
updated to match a duplicate implementation, and the latter changed into
a call to compareModelSpecies() instead.

Might need some tweaking in the future of what "identical" and "similar"
means for thermo data.
Small changes to chemkin output.

Colliders are hopefully sorted (to reduce random diffs between identical
models) and kinetics comments have an extra line break if the barrier
was raised.
Add fromSMILES method to Species class.

This was used in some of the old unit tests.
Attempt to fix old unit tests in unittest/rmg/ folder

Some of these seem very broken. I am wondering how many of them have been sufficiently
replaced with the tests in the higher level folder that these can be discarded?
Some more attempts to fix unit tests. These are really broken!
Formatting changes for long lines.

Trying to follow the python style guide
http://www.python.org/dev/peps/pep-0008/
Allow Arrhenius objects to store applicable pressure range
Merge branch 'master' of github.com:GreenGroup/RMG-Py