[lammps-users] How to determine Aluminum oxide layer thickness in Reactive MD simulation in LAMMPS?

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1

I am simulating formation of Aluminum Oxide layer at room temperature in LAMMPS. The simulation is reactive, meaning the initial configuration, which consists of Al nanocluster, encapsulated with Oxygen gas will react according to the Streitz-Mintmire forcefield. I can see oxide layer forming on visualizing my dump file but I do not know yet how to measure the thickness of the oxide layer. Can this be written into lammps input script or is there a post-processing tool that can determine this effectively? Does anyone have an idea?

Regards,

Emmanuel Olugbade

Graduate Research Assistant, AEMS Lab

PhD candidate, Mechanical Engineering

Missouri University of Science and Technology

258B Toomey Hall, 400 W. St, Rolla, MO 65401

2

This is not trivial to do, will not be very precise, and dependent on your choices and definitions.

There is the principal problem of the size of an atom being an ill-defined property.

Next you need to find a way to identify the atoms that comprise the oxide layer, for which there is no clear distinction (how can you tell whether an oxygen atom has reacted or is just adsorbed?).

From there it would be a question of how you define the thickness: min-max of positions or derived from the density (mass or number?). One way to do this would be to do a 1d-density profile and then use some measure where to place the cut (e.g. half-height of where the gradient changes the sign).

Axel.

3

It is one way to get a density profile.
Whether it is the best I am not able to say. That depends on the details and your needs and skills.
There are packages specifically written for the analysis of MD simulation data and there always is the option to write a custom script to do exactly what you want to compute.

4

Thanks for your reply. To get the 1d density profile, is using the “compute chuck/atom” and “fix ave/chunk” the way to go or there is a better approach to it?

Regards,

Emmanuel Olugbade

Graduate Research Assistant, AEMS Lab

PhD candidate, Mechanical Engineering

Missouri University of Science and Technology

258B Toomey Hall, 400 W. St, Rolla, MO 65401

5

Thank you Axel. I was able to identify the oxide layer thickness and it corresponds to values reported in literature.

Regards,

Emmanuel Olugbade

Graduate Research Assistant, AEMS Lab

PhD candidate, Mechanical Engineering

Missouri University of Science and Technology

258B Toomey Hall, 400 W. St, Rolla, MO 65401