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how can I visualize bond for my custom dump trajectory files

Hi everyone,

I can use Ovito to visualize the lammps data file and the bond will be visualized in the Ovito. But when I try to visualize my custom lammps trajectory file (lammps command: dump 1 all custom 1 nvt.lammpstrj id type x y z vx vy vz fx fy fz ), the bond information will not be shown in the software. Is it due to my custom lammps trajectory file does not contain the bonding information as my data file?

How can I visualize the  bonding information while I see my custom lammps trajectory files in Ovito?

Attachments are the read-to-run corresponding files and corresponding images.

Thanks!

******************************************************************
Dezhao Huang
Ph.D. candidate at University of Notre Dame
Department of Aerospace and Mechanical Engineering
B14 Fitzpatrick Hall
Notre Dame, IN 46556-5710
Tel: (573)-578-0869
dhuang2@nd.edu

 

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Dear Dezhao,

your lammps-dump file doesn't contain any bond information, so what you're describing is the expected behavior.

You could use a Create Bonds modifier to generate and visualize the bonds in OVITO. Simply edit the pair-wise cutoffs table in the modifier settings and insert the values that correspond to your system.

Since you already have a lammps-data file with the bond information, you have another option:  First import the lammps-data file in OVITO and then use a Load trajectory modifier to merge the bond information with your lammps-dump trajectory.

Let me know if that works for you.

-Constanze

Thank you Constanze! The second method you recommend can solve my problem!

Best,

Dezhao