Added the input writer to the MopacPM3 method.
Added the input writer to the MopacPM3 method.

The methods will be seperated based on program. So the
input writer, job runner, verifier, etc. will all be
together.
faribas/RMG-Py,nyee/RMG-Py,enochd/RMG-Py,comocheng/RMG-Py,nickvandewiele/RMG-Py,comocheng/RMG-Py,nickvandewiele/RMG-Py,nyee/RMG-Py,faribas/RMG-Py,chatelak/RMG-Py,enochd/RMG-Py,pierrelb/RMG-Py,KEHANG/RMG-Py,KEHANG/RMG-Py,pierrelb/RMG-Py,chatelak/RMG-Py