Documentation additions

documentation/source/users/rmg/database/modification.rst

@@ -264,4 +264,12 @@ Be sure to give errors whenever adding rules. If you don't know the uncertainty,
 why do you trust the kinetics?
 
 After you are done always check via populate reactions or the website, that your
-modifications are behaving the way you expect.
+modifications are behaving the way you expect.
+
+Caveat regarding how rate rules are used by RMG and the rate parameters you input: because tunneling is
+important for many chemical reactions, the rate of a reaction may not be easily represented by
+a bi-Arrhenius fit. 3-parameter fits are more common. However, the resulting fit may report an
+'activation energy' that is much different (possibly by 10+ kcals) than the the true barrier height. 
+When RMG is assembling pressure-dependent networks, it will use barrier heights from rate rules. This can 
+lead to very inaccurate rate calculations. To avoid this issue, try to ensure that your fitted arrhenius 
+activation energy truly does reflect the reaction barrier height. 

documentation/source/users/rmg/input.rst

@@ -337,6 +337,17 @@ Miscellaneous options::
 		generatePlots=False,
 	)
 
+	generatedSpeciesConstraints(
+        maximumCarbonAtoms=10,
+        maximumHydrogenAtoms=10,
+        maximumOxygenAtoms=10,
+        maximumNitrogenAtoms=10,
+        maximumSiliconAtoms=10,
+        maximumSulfurAtoms=10,
+        maximumHeavyAtoms=10,
+        maximumRadicalElectrons=10,
+	)
+
 Examples
 ========
 

documentation/source/users/rmg/installation/linux.rst

@@ -23,7 +23,7 @@ The instructions listed below have been confirmed on a fresh Ubuntu 12.04 instal
 
 	sudo pip install numpy		# install NumPy before other packages
 
-	sudo pip install scipy cython nose matplotlib quantities guppy sphinx psutil xlwt
+	sudo pip install scipy cython nose matplotlib quantities guppy sphinx psutil xlwt freetype2 libpng-dev
 
 	cd ~
 	git clone git@github.com:jwallen/PyDAS.git

documentation/source/users/rmg/output.rst

@@ -3,4 +3,13 @@
 **************************
 Analyzing the Output Files
 **************************
-
+
+You will see that RMG has created multiple output files and folders: ::
+	:file:'/chemkin  input.py output.html  /pdep  /plot  restart.pkl  RMG.log  /solver  /species'
+
+The :file:'/chemkin' folder will likely have a large number of chemkin formatted files. In general, these can be disregarded, as you will be mainly interested in :file:'chem.inp', the chemkin formatted input file with a species list, thermochemical database, and a kinetic mechanism. The file :file:'chem_annotated.inp' is provided as a means to help make sense of species syntax and information sources. In addition, a species dictionary,:file:'species_dictionary.txt', is generated. Either chemkin file, in addition to the dictionary, may be used as inputs in the tools section of this website to better visualize the species and reactions: http://rmg.mit.edu/simulate/chemkin  
+(alternatively, you can open :file:'output.html')
+
+The :file:'/pdep' folder will contain files associated with the pressure-dependent reactions that RMG has generated. These files are formatted as input files for CanTherm. 
+
+RMG currently includes a solver for isothermal batch reactors. This is in fact a critical part of the model enlargement algorithm. If you have included simulations in your input file, the solutions will be located in :file:'/solver'. You will probably only be interested in the files with the largest number tags.  

documentation/source/users/rmg/running.rst

@@ -3,4 +3,11 @@
 *************
 Running a Job
 *************
-
+
+ Submitting a job is easy ::
+
+	python rmg.py input.py
+
+We recommend you make a job-specific directory for each RMG simulation. Some jobs can take quite a while to complete, so we also recommend using a job scheduler (if working in an linux environment). 
+
+