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Automatic re-evaluation of the simulation cell after loading a trajectory for a Lammps data file

Hello,

I use a fixed data file containing all the topology information; however, for each set of simulations, I change box size by change_box command in my lammps input script - all the simulations have the same topology but different box size.

In Ovito, I  use this data file for all the separated sets of the simulations to have the topology (bond) information but later I want to change the simulation cell information based on the imported set of trajectories. Currently, I manually update the simulation cell information. Is there any way to tell Ovito to update the simulation cell dimension based on the imported trajectory within a data (topology) file?

I use the free version of Ovito.

Thanks in advance for your help.

 

Hi Amir,

I'm not sure if I fully understand the situation you describe. When you talk about topology and trajectory information, you must have two types of files, a LAMMPS data file (a.k.a. topology file) and a LAMMPS trajectory dump file, right? You don't mention it, but are you using the Load Trajectory modifier to load these two files into the program? Because if you do, OVITO should already use the current simulation box size read from the LAMMPS dump file, overriding the initial box size loaded from the LAMMPS data (topology) file.

I'm sorry if I didn't get the problem you a trying to describe. Please specify which file(s) are involved and how you do load them into OVITO. Then I'll assist you in solving the problem. Thanks.

-Alex

Hello Alexander,

Sorry for my bad explanation. As you described, I first open a Lammps data file (topology: bond style) and then add a Lammps trajectory (dump) for that via the add trajectory in the modifications toolbar.

The simulation cell's bounds in data file is different from those in the trajectory file (but they have the same topology (particles, bonds, ...) information).  After adding the trajectory, the simulation cell's information (x, y,z bounds) are still those of the data file and are not updated to those in the trajectory file . To solve this issue, I manually change the box size or cell vectors in the simulation cell window.

Is there anyway that Ovito do this automatically?

Thanks for your quick response.

Amir

It sounds like you are already doing the correct thing. But then I am surprised that you do not see OVITO picking up the new cell size from the trajectory dump file. The Load Trajectory modifier is supposed to overwrite the static cell size from the topology data file with the (possibly varying) cell size information from the trajectory dump file.

What happens if you open just the trajectory dump file directly in OVITO (without loading the topology file and without using the Load Trajectory modifier)? Do you then see the correct box size?

In that case, I have the correct simulation cell information but obviously without the bond information.

 

Please find attached a copy of the data file and a truncated copy of the dump file I use for this purpose.

Thanks for your help.

Uploaded files:

Thanks. I've opened your files in OVITO, and it seems to work as expected. Once I apply the Load Trajectory modifier and pick the trajectory dump file, the displayed simulation box is updated and becomes taller than the initial box from the data file. Please see the attached screenshot and compare the program state to yours.

 

Uploaded files:
  • Screenshot-2020-08-08-at-18.53.04.png

Thanks for your strong support. That's correct! I got confused since I checked the Box box and Cell geometry  under the Simulation cell window which itself is a subcategory of the imported data file under the input section. It is reasonable  that the information there should be related to the data file that is imported as the main file. But, what about the information about the simulation cell which is read from the trajectory file that itself is added to the data file? Should we somewhere see this updated information about the simulation cell as a warning or summary or ... ?

Can this be a new feature/functionality for Ovito if it is not already implemented?