Generation .data files with charges using OVITO

LAMMPS LAMMPS Beginners
1

Greetings to all LAMMPS users. I’m new to molecular dynamics and have encountered a problem creating an input file for LAMMPS (.data) containing both atomic coordinates and their charges (since I plan to study ionic structures). Can I create this file using OVITO? I found several examples with data files that contain the following lines:

# LAMMPS data file written by OVITO Basic 3.3.5
3000 atoms
3 atom types
0.0 28.7403 xlo xhi
0.0 28.7403 ylo yhi
0.0 86 zlo zhi

Masses

1 52.0 # Cr
2 55.84# Fe
3 16.0#O

Atoms #charge

1 2 -0.00261781 0.0 0.0 0.0
2 2 -0.00267272 1.43701 1.43701 1.43687
3 2 -0.00102195 2.87403 0.0 0.0
4 2 -0.00406443 4.31105 1.43701 1.43687
...
2999 2 -0.00459523 25.8663 25.8663 40.2362
3000 2 -6.75683e-04 27.3033 27.3033 41.6735

Do I understand correctly that such a file can be obtained using OVITO without using third-party software, if so, how? I spent a lot of time searching for information about creating a material structure in OVITO for the purpose of later exporting to a .data file, but I didn’t find anything.

I would be grateful for links to any manuals, tutorials, etc. that would help me understand the creation of .data with coordinates and atomic charges using OVITO.

2

Since your questions are all about OVITO, you may be better off asking them in the OVITO category.

Tutorials on learning how to use LAMMPS and how to build systems for use with LAMMPS are listed on the LAMMPS homepage. You may also have a look at the material of the LAMMPS workshops. There also is a page for tools that can be used for pre-/post-processing LAMMPS data.

3

Thanks for such a quick response. Yes, I was researching about tools that can be used for pre-/post-processing and found a very simple tool called Atomsk. But what confuses me is the fact that in the example described in section “5. Add electric charges” (https://atomsk.univ-lille.fr/tutorial_lammps.php) the charges corresponding to a certain type of atom (1 or 2 in this case ) are absolutely equal to each other, which cannot be said about the example, a fragment of which I attached earlier.
Accordingly, the question arises: how physically/chemically is it justified that atoms of the same type in an alloy can have charges of different values? (I apologize if this question seems strange, this type of calculation is just completely new to me).

4

The example you showed was for an oxide not an alloy. Force fields for oxides typically require the use of charge equilibration since the polarization is different for atoms within the bulk and near/on the surface and also different cations may be differently polarizable by the oxide.

That said, the initial data file for such an oxide calculation may have started with identical charges and only after applying the charge equilibration, may the data file look like in the quoted example.

1 Like
5

This is very interesting and logical, thanks for the explanation. In this case, what tools and/or methods can be used to obtain a equilibration charge distribution?

6

LAMMPS.

7

Thank you very much for the discussion, I naively believed that the problem with different charge values was in the way the initial .data file was generated and OVITO would help me solve this problem.