logging and output

* difference between print and logging

There are three options for logging in RMG. 'Quite', 'Verbose' and 'Debug'.

For 'Quite' option: Terminal will print nothing, so does RMG.log. But when there are some warnings and errors, terminal will print them, but will not output to RMG.log file.

Default Option: Print input file, and then information about loading thermo libraries, transport libraries, and thermo group database, transport database, kinetic families, frequencies group databases, Platts additivity group databse For 'Verbose'

* how files, graphs, etc are saved
* methods RMG uses to display molecules, reactions, etc. in ipython notebook and website