Molecular dynamics with Asap and ASE

Typical computer simulations involve moving the atoms around, either to optimize a structure (energy minimization) or to do molecular dynamics. The Atomic Simulation Environment (ASE) defines a number of object doing just that. Documentation of these methods can be found on the page called Molecular Dynamics in the ASE online documentation.

Using ASE Molecular Dynamics objects with Asap

The standard ASE molecular dynamics objects can directly be used with Asap simulations, except if the Asap simulation is on a parallel computer, where some of the objects will fail. To handle this situation, special versions of most of the ASE dynamics objects are provided, which are modified to handle both serial and parallel simulations. We recommend always to use the Asap-provided dynamics objects, also for serial simulations. In that way you will not forget to modify your script when switching to parallel simulations, and you will benefit from any Asap-specific optimizations.

The Asap molecular dynamics objects are used exactly as the ASE version, as documented on the ASE Molecular Dynamics page. The only difference is that you should import them from asap3.md instead of from ase.md, i.e. replace

from ase.md.verlet import VelocityVerlet

with

from asap.md.verlet import VelocityVerlet