Which free available simulation software is there which could help simulate ion path after they are released from a source under action of magnetic and electric and other fields and depending on the angle they are released at?
Honestly I don't think its possible to have a free software to do that simulation,but you can always use COMSOL Multiphysics for quick simulation with 30 days trial.
If you need full physical detail, there is always geant4 and similar simulation engines from particle and nuclear physics, that are quite suitable for the purpose.
Perhaps it would be better to specify the context in which you want to solve the problem. In high-energy physics there are opensource software frameworks for simulating collision processes and propagation of any sort of particle through vacuum and matter. For example, Geant4 is a well-known C++ framework developed at CERN, which can be well interfaced with ROOT for visualization, storage, and data analysis, another opensource software from CERN. On the other hand, if you want to trace ions propagating through the Galaxy and interacting (spallation process) with the interstellar medium (mostly protons), then you may prefer to look at what has been produced by the cosmic-ray community (GALPROP is a well known numerical approach, but there are alternatives that use semi-analytic computation of the diffusion equation). Another possibility is ion interaction with the upper atmosphere, in which case the cosmic-ray community is still your place to look at, although this time you need to search for shower development.
BTW, if you only need to trace it through magnetic and electric field, you can solve the problem directly :-) The trick is to get the equation of motion and pick any existing opensource software for solving the differential equation. As there are no interactions in this case, using the packages above might look like overkilling.