AtomEye

AtomEye is atomistic visualization software fast enough to handle output of molecular dynamics simulations with millions of atoms. It includes parallel and perspective projections with full three-dimensional navigation, customizable bond and coordination number calculation, colour-encoding of arbitrary user-defined quantities, local atomic strain invariant, coloured atom tiling and tracing, up to 16 cutting planes, periodic boundary condition translations, JPEG, PNG, and EPS screenshots, and animation scripting.