Documentation: QM options in the input file

Hopefully this is clear. Highlighted the external programs
linked with QM (Gaussian, MOPAC, RDKit). Also gave an
example script to include in the input file.

Author: pierrelb

documentation/source/users/rmg/input.rst

@@ -213,6 +213,36 @@ The following is an example of a simple reactor system::
 On the fly Quantum Calculations
 ===============================
 
+This block is used when quantum mechanical calculations are desired to determine thermodynamic parameters. 
+These calculations are only run if the molecule is not included in a specified thermo library.
+The ``onlyCyclics`` option, if ``True``, only runs these calculations for cyclic species.
+In this case, group additive estimates are used for all other species.
+
+Molecular geometries are estimated via RDKit [RDKit]_.
+Either MOPAC (2009 and 2012) or GAUSSIAN (2003 and 2009) can be used
+with the semi-empirical pm3, pm6, and pm7 (pm7 only available in MOPAC2012),
+specified in the software and method blocks.
+A folder can be specified to store the files used in these calculations,
+however if not specified this defaults to a `QMfiles` folder in the output folder.
+
+The calculations are also only run on species with a maximum radical number set by the user.
+If a molecule has a higher radical number, the molecule is saturated with hydrogen atoms, then 
+quantum mechanical calculations with subsequent hydrogen bond incrementation is used to determine the
+thermodynamic parameters.
+
+The following is an example of the quantum mechanics options ::
+
+	quantumMechanics(
+		software='mopac',
+		method='pm3',
+		fileStore='QMfiles',
+		scratchDirectory = None,
+		onlyCyclics = True,
+		maxRadicalNumber = 0,
+		)
+
+.. [RDKit] RDKit: Open-source cheminformatics; http://www.rdkit.org
+
 Pressure Dependence
 ===================