In Materials 7.0, we added a new keyword for Forcite and Mesocite to the MaterialsScript API called ExternalForceStrength. This allows a user to place a constant force on a set of atoms or beads. If you want to calculate the diffusivity for a molecule larger than methane, the dynamics time is too long for a simulation. Hence, an external force can be used to "push" a large molecule through a polymer matrix thus estimating the diffusivity of that molecule in the matrix.

If you just calculate the diffusivity from the mean-squared displacement, this still includes the force. To estimate the diffusivity more accurately, you can allow for the force by calculating the drift velocity and then obtaining the diffusivity from the drift velocity. This requires you to extract the coordinates of the center of mass of the penetrant molecule and calculate the drift velocity.

I have written a short script which takes the trajectory, external force set name, external force, and temperature as input. From this, the drift velocity and diffusivity can be estimated.

As with all diffusivity calculations, the trajectories tend to be very large and hence I have not included an example input file.

Have fun!

Cheers

Stephen