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.
Added global Initialize System Property

This function was not updated with Richard's changes
to specify working and scratch directories. Updated
function to call global.InitializeSystemProperties()
Merge branch 'master' of github.com:GreenGroup/RMG-Java
Added some release notes and documentation for 4.0.1 bug-fix release.

Download links, templates, settings file, etc. etc. have not been updated.
Updated comments in RMG example batch scripts to reflect latest release version.
Added RMG example bash script files for linux users.
Changes to documentation and web source to reflect v4.0.1 upgrade.
Added Some of the JP10 Libraries
Finished Adding JP10 Libraries
Libraries for v0.7 of JP10 added
Adding rate rules for olefin + HO2 radical addition

Reference:
Rate rules, Branching Ratios, and Pressure Dependence of the HO2+Olefin Addition Channels
http://pubs.acs.org/doi/abs/10.1021/jp405262r
Paper uses CBS-QB3 energy w/1D-HR calculations, refer to Table 2 for the rules.
Adding rate rules for ROO = olefin + HO2

Reference:
High pressure rate rulesfor Alkuly+O2 reactions: 1
http://pubs.acs.org/doi/pdf/10.1021/jp2079204

Refer to Table 4 for rate rules
uses CBS-QB3 w/1D-HR calculations, since the sumathy
rates and rates calculated by stephanie villano are
using the same method for energy and hindered rotors
they have the same rank for now.
Fixed typo in the rate rules

Typo in rate rules for HO2 elimination from peroxy
Fixed incorrect definition for group "OJ" instead of having duplicate of "OsJ".
Adding rate rules for intra-H migration for alkoxy radicals

These rules are made from the butoxy and hydroxybutyl system calculated at
RQCISD(T)/CBS//B3LYP/6-311++G(d,p) level.

Ref Ab Initio Kinetics for the Decomposition of Hydroxybutyl and
Butoxy Radicals of n-Butanol.
by: Zhang P.,Klippenstein S.K.,Law C.K.
dx.doi.org/10.1021/jp400155z | J. Phys. Chem. A 2013, 117, 1890-1906

Note some of rate rules were given as sum of two Arrhenius,they were
refitted to single Arrhenius
Adding rate rules for Beta-scission of alkoxy radicals

These rules are made by reversing the rules from the butoxy and
hydroxybutyl system calculated at RQCISD(T)/CBS//B3LYP/6-311++G(d,p) level.
The thermochemistry used comes from n-butanol mechanism
dx.doi.org/10.1016/j.combustflame.2010.06.002.

Ref Ab Initio Kinetics for the Decomposition of Hydroxybutyl and
Butoxy Radicals of n-Butanol.
by: Zhang P.,Klippenstein S.K.,Law C.K.
dx.doi.org/10.1021/jp400155z | J. Phys. Chem. A 2013, 117, 1890-1906

Note: some of rate rules were given as sum of two Arrhenius,they were
refitted to single Arrhenius