QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: AsifShah on October 24, 2023, 05:55

Title: Atoms going out of simulation box
Post by: AsifShah on October 24, 2023, 05:55

Dear Admin/All,
I was running some heating simulations on gold. After it becomes amorphous at melting point the atoms move outside simulation box. how to avoid this? Though the atoms in MD trajectory dont go out of simulation box but when I send last trajectory to builder or viewer it goes outside box.
Please see attached images.

Title: Re: Atoms going out of simulation box
Post by: Anders Blom on November 2, 2023, 01:54

This is perfectly normal, the atoms have no reason to stay in the original unit cell if the temperature is high enough. Especially in order to track quantities like mean square displacement, you have to let the atoms travel outside the box and not just wrap them by periodic boundary conditions. If you still prefer that for your animation, you can choose it in the Movie Tool buy right-clicking and choosing "Wrap atoms".

Also you can always wrap a structure in the Builder, there is a tool for it under Bulk Tools.

Title: Re: Atoms going out of simulation box
Post by: AsifShah on November 2, 2023, 09:55

Thanks a lot.