logging and output

• difference between print and logging

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

Default Option: Print information is same as log file. The logic is like this: Print input file information, and then simple information that RMG are loading thermo libraries, transport libraries, and thermo group database, transport database, kinetic families, frequencies group databases, Platts additivity group databse. Then terminal prints information that RMG are adding rate rules from training set in kinetic families. Then terminal will print how RMG calculate the thermo data of specific species, from thermo library or group additivity. Thermo library is always first choice, or RMG will print all possible resonace isomers and their thermo estimates when using group additiity. Then terminal will give summary of model enlargement, about new core species, new edge species, new edge reactions, and output infomration about estimating thermo and kinetics of new created species. Current model is saved to file. RMG then will conduct simulation of reactor systems and see if the termination rule is met. Above steps will be done and output repeately until final mechanism is generated. RMG will automatically add AR, He, Ne and N2 to core in the first model enlargement. And the RMG will begin the iterative calculation with species given in inupt.py, new species and reactions. Finally, terminal output information of final mechanism, about numbers of core species and reactions, as well as same infomration about edge species and reactions. Execution time and memory usage will also be output.
For 'Verbose' option: Print information is same as log file. Compared to Default option, terminal will provide much more details about where to load kinetics family groups and rules. After summary of model enlargement, terminal will provide infomration about new species and new template reaction before estimating thermo of these new created species.

For 'Debug': Print information is same as log file. Compared to Verbose option, terminal will not only provide much more details about where to load kinetics family groups and rules, but also provide details about how to find the specific kinetics group when kinetics family groups are loading. But it will only give us memory address, so it still need improvement to make more helpful for 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.

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