Hi, sorry for later reply.
You will simply take the whole container and prescribe your desired vibration. See the impose tutorial on how to do it.
You can attach the same Impose to multiple nodes, so let's say your cylinder is composed of flat caps and triangulation around, you can attach the vibration to all those particles individually, or, which is perhaps more readable, add the whole cylinder using addClumped as shown in the bottle example. You might need to create a "handle" node if the cylinder has no mass explicitly, and then prescribe vibration to that node.
As to what subclass of Impose to use, check out the possibilities here, it depends whether you want also rotation. For translations, you can readily use HarmonicOscillation or perhaps VariableVelocity3d, which is very flexible and lets you vibrate in 3 senses simulatneously. Also note you can add impositions together (with +) so you can e.g. have 3 perpendicular HarmonicOscillations applied to that single node (see e.g. here).
During the vibration phase (if you have not done so before), it is advisable to set friction angle to zero to achieve maximum compaction.
Hope this helps,