Save output before first simulation run.
Save output before first simulation run.

If the first simulation fails, it would be nice to see the mechanism that
caused the failure. 
There is a new method saveEverything that saves the HTML, Chemkin, and restart.
This is now called at the start as well as once per iteration.
chatelak/RMG-Py,comocheng/RMG-Py,nickvandewiele/RMG-Py,nickvandewiele/RMG-Py,chatelak/RMG-Py,faribas/RMG-Py,enochd/RMG-Py,faribas/RMG-Py,comocheng/RMG-Py,pierrelb/RMG-Py,pierrelb/RMG-Py,nyee/RMG-Py,enochd/RMG-Py,KEHANG/RMG-Py,KEHANG/RMG-Py,nyee/RMG-Py