Visualizing ellipsoid in OVITO

OVITO General questions
1

Dear OVITO team,

I’m trying to visualize the LAMMPS data file which contains ellipsoid features with OVITO. When selecting the LAMMPS atom style as ellipsoid when opening the data file with OVITO, I got an error that :
" the atom style of the LAMMPS data file cannot be detected … " .

I would appreciate to help me with visualizing ellipsoid data file.

here is the header and the body of the data file :

LAMMPS Description

5000 atoms
5000 ellipsoids
0 bonds
0 angles
0 dihedrals
0 impropers

1 atom types

-26.6439 26.6439 xlo xhi
-26.6439 26.6439 ylo yhi
-26.6439 26.6439 zlo zhi

Atoms
atom-ID atom-type x y z atom-ID ellipsoidflag density
.
.
.
Ellipsoids
atom-ID shapex shapey shapez quatw quati quatj quatk
.
.
.

2

Hi, please excuse the late reply. While OVITO can load and visualize ellipsoid particles from LAMMPS dump files (see here), the support for the “ellipsoid” variant of the LAMMPS data file format may still be incomplete. We can work on completing the support for this type of files. It would be useful if you can provide your complete data file as an example. Thanks.

-Alex

3

Dear Alex,
Thanks for the response. Yes I had no problem visualizing the ellipsoid from the LAMMPS dump file with OVITO, but the problem is visualizing the DATA file as well. I’m trying to upload the DATA file, but I got the error that “new users are not allowed to upload a file”!
How can I send you my DATA file?

Thank you in advance,
Reyhaneh

4

I’m sorry I missed your message.
I’ve raised your trust level in the forum now, which should allow you to upload a file.

5

Thanks Alex,
Here is an example of an ellipsoid DATA file.
tip4p.data (866.8 KB)

6

Hi,
Thanks for providing the data file. The columns in the Atoms section of that file seem to be in the wrong order. You wrote above that the columns are in the following order and that the simulation uses the ellipsoid atom style of LAMMPS:

atom-ID atom-type x y z atom-ID ellipsoidflag density

However, the documentation of the LAMMPS read_data command says that the column ordering for atom style ellipsoid is supposed to be as follows:

atom-ID atom-type ellipsoidflag density x y z

This is also what OVITO expects. Do you have any explanation for this discrepancy? I am wondering which software was used to write the data file.