getting a data file for al2o3

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1

I am trying to create a supercell of Fe2o3. Based on my reading I made one crystal in avogadro, then saved as pbd. I then used vmd to load in the molecule and topotools to make it as a lammps file atom style full.

I want this potential to be used in reaxff, but this file from topotools included info on bond and types and some other data that based on other reaxff data files I should not need. Is it just as simple as then modifying that data file for a reaxff data file, or is there another way I should make data files for crystals. I found some examples of other crystal data files, what software was used to make these?

https://github.com/lammps/lammps/blob/master/examples/reax/FeOH3/data.FeOH3

Below is my data file for Fe2O3

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 on Fri Jul 20 13:04:39 -0230 2018
16 atoms
2 atom types

3.093000 8.523000 xlo xhi
0.809918 5.273081 ylo yhi
0.000034 4.158966 zlo zhi

Masses

1 15.999400 # O
2 55.845001 # FE

Atoms # full

1 1 2 0.000000 1.220000 0.639000 0.437000
2 2 1 0.000000 3.775000 3.160000 0.000000
3 3 2 0.000000 4.588000 2.403000 1.643000
4 4 2 0.000000 10.396000 5.444000 3.722000
5 5 2 0.000000 7.027000 3.680000 2.516000
6 6 1 0.000000 3.093000 2.450000 2.945000
7 7 1 0.000000 4.748000 0.473000 1.214000
8 8 1 0.000000 6.490000 1.738000 2.079000
9 9 1 0.000000 5.125000 3.514000 3.294000
10 10 1 0.000000 5.808000 3.872000 0.865000
11 11 1 0.000000 4.748000 1.303000 0.000000
12 12 1 0.000000 3.093000 3.633000 1.214000
13 13 1 0.000000 3.775000 1.147000 2.945000
14 14 1 0.000000 5.125000 4.345000 2.079000
15 15 1 0.000000 6.490000 2.568000 0.865000
16 16 1 0.000000 5.808000 2.211000 3.294000

2

Please see https://lammps.sandia.gov/prepost.html for crystal building tools listed under “GUI and Analysis Software”.

By the way, you Fe2O3 doesn’t look correct as a R-3C unitcell contains 30 atoms.

3

Thanks Ray,

That is very interesting. I go into avogadro, import the Fe2O3 crystal and this is what I get for atom coordinates. What makes even less sense is why I have 4Fe and 12O, which is not the correct ratio? When I try Al2O3 the ratio is correct. Could this be a bug in Avogadro?

Liam

4

When speaking with some avogadro people on that forum they say the reason for this is because oxygen atoms are at the corner and are counted as a half. Is there any error in importing the crystal into avogadro, saving as pdb, loading pdb into vmd, using topotools to make data file, then replicating in lammps to get a supercell?

It appears avogadro uses the primitive unit cell and not the conventional unit cell that would have 30 atoms?

5

Atoms sharing corners, edges, or faces are the same atom due to symmetry hence there should only be one. Avogadro being a molecular builder is not getting the crystallography of Fe2O3 (R-3c) correct. R-3c has 2 Wyckoff positions at 18e and 12c – meaning the smallest unitcell has 30 atoms.

This is not a LAMMPS question so excuse me for not responding any further.

6

Yes, the primitive cell of Fe2O3 (R-3c) has 10 atoms.

7

Ok thanks for your help again Ray. To be clear, if Avogadro is getting the primitive unit cell right am I ok to export that as a pdb, use topo to make it into a lammps file, then replicate this primitive until cell. Or should replication only be done on the conventional unit cell of 30 atoms?

Thanks

Liam