Added examples for SCOOP and some minor improvements

Author: keceli

README.scoop

@@ -0,0 +1,21 @@
+******************************************************
+SCOOP enabled RMG-Py
+******************************************************
+
+RMG-Py can be run in parallel (only for the thermochemical parameter 
+estimation part) using SCOOP module.
+More info on SCOOP: http://code.google.com/p/scoop/
+
+Running RMG-Py in parallel:
+
+python -m scoop.__main__  -n 8 $RMGpy/rmddg.py input.py > RMG.sdout.log &
+
+-n 8 specifies that you will have 8 workers. 
+Set it based on the available number of processors.
+For job submission scripts check examples/rmg/scoop.
+
+Installing SCOOP:
+
+You need the development version of SCOOP (tagged with 0.7RC2).
+Download link: http://scoop.googlecode.com/archive/0.7RC2.zip
+

README2SCOOP.rst

@@ -0,0 +1,2 @@
+#!/bin/bash
+source ~/.bash_profile

examples/rmg/scoop/prolog.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+#####################i################################################
+# This is a job submission file for a SGE queuing system to run
+# the SCOOP-enabled parallel version of RMG-Py across 48 CPUs on
+# a single node.
+#
+# Define RMGPy as the path to rmg.py in your ~/.bash_profile
+# NSLOTS is an SGE env. variable for total number of CPUs.
+# prolog.sh is a script used by SCOOP to pass env. variables
+#
+# You can run the jobs on different nodes as well, but it is not
+# recommended since you might have problems with SGE job termination.
+# Type `qconf -spl` to see available parallel environments and modify
+# the last #$ line if you really want to run it on many nodes.
+#####################i################################################
+#$ -S /bin/bash
+#$ -cwd
+#$ -notify
+#$ -o job.log -j y
+#$ -N RMGscoop
+#$ -l normal
+#$ -l h_rt=09:05:00 
+#$ -pe singlenode 48
+source ~/.bash_profile
+python -m scoop.__main__ --tunnel --prolog $RMGpy/examples/rmg/scoop/prolog.sh  -n $NSLOTS $RMGpy/rmg.py input.py > std.out