Building the sphere filled with Al2O3

LAMMPS LAMMPS General Discussion
1

Dear All,

I found that the ‘region sphere’ command could build up the sphere filled with one type atom. Is there any command in lammps building up the sphere structure filled with compounds; such as, alpha phase-Al2O3?

I want to build up a box structure filled with many spheres. Each sphere is filled with alpha-phase Al2O3. Beteween each sphere, this are some spaces filled with benzene rings.

Does LAMMPS have any command to build up such structure?

If so, which command can build up such structure?

If not, how could I simulate such system with LAMMPS?

Thank you in advance.

2

Hello,

I am sure that this can be done using only internal LAMMPS commands, in particular:

  • lattice to help placing the Al2O3 atoms at the right location,
  • region to help delimit the spheres,
  • molecule to help create benzene rings,
  • create atoms to insert the Al2O3 atoms and benzene molecules.

However, given the complexity of your system, using an external tool or just a home-made script to generate the initial topology would probably be simpler.

Simon

3

Building objects from \mathrm{Al}_2\mathrm{O}_3 is not quite as simple since it is an oxide.

When cutting objects from the lattice, you need to watch out so that you don’t create highly polar (and thus high-energy) surfaces that would lead to significant reconstruction or are not stable. Also, you need to make sure that the system is neutral, and in some cases this will likely mean that dangling bonds are saturated with hydrogen atoms. The choice of force field is also much more important to get correct results than for bulk systems, where you don’t have to worry about the surfaces.

Then finding a compatible set of force field parameters for your interaction with benzene is another challenge.

Overall, this is not a project suitable for someone with limited experience in setting up and performing MD simulations. There are many, many possible sources for (sometimes small) errors that can add up and make the whole effort a waste of time due to producing meaningless results.

For certain, the first step should be some research into what are stable structures and geometries for some smaller nanostructures.

4

Thank you for your suggestions.

Is there any example case for building up similar structure with LAMMPS command that I can refer to? Would you please recommend some examples if someone has already done such work before?

Thank you again.

5

Thank you for your comments and all possible difficulties that I may encounter.

I will think about all these issues carefully.

6

You can use a tool like the following one to create a spherical NP of desired radius which is electrically neutral

https://www.enaloscloud.novamechanics.com/riskgone/nanoconstruct/

It is free and quite easy to use.

HTH
Evangelos

1 Like
7

Thank you for your suggestion.

Would you please give me some more suggestions?

If each sphere is filled with Al2O3 and the Al2O3 is covered by a bi- or tri- layer graphene, how to build up such kind of composite sphere?

How distribute this composite sphere randomly within the box region for LAMMPS simulation?

How to fill the space between these randomly distributed spheres with the benzene rings?

Thank you again.

8

I don’t know any tool to wrap the spherical NP with graphene. Most likely you have to write your own tool.

To insert randomly the NP and benzene molecules in a simulation box, you can either use the create_atoms command as @simongravelle has pointed out or use packmol (an external tool listed in lammps website for preprocessing software)

HTH, Evangelos