Messages

1

Scripts, Tutorials and Applications / Re: How to Apply Heat Flux in NEMD Simulations Using the "Exchange Interval" Option

« on: October 18, 2025, 08:31 »

Hello QuantumATK team,

Thank you for your guidance; the process is now clear to me. I go through the reference image attached showing a temperature profile analysis for SiO₂ quartz (MTP pretrained, RNEMD) using the Molecular Dynamics Analyzer in QuantumATK.
Could you please share the official documentation or example workflow/script that explains how to set up and perform the RNEMD (Reverse Non-Equilibrium Molecular Dynamics) simulation for SiO₂ using the MTP potential and generate and fit the temperature profile as shown in this plot?

Any references or sample Python scripts for automating this process in the QuantumATK Script Generator would be very helpful.

Thank you in advance for your guidance!

2

Scripts, Tutorials and Applications / How to Apply Heat Flux in NEMD Simulations Using the "Exchange Interval" Option

« on: July 22, 2025, 07:59 »

Hi all,

I'm setting up a non-equilibrium molecular dynamics (NEMD) simulation in QuantumATK to calculate the thermal conductivity of a material. I understand that QuantumATK allows heat flux to be imposed by exchanging kinetic energy between two regions (hot and cold) using the "Exchange Interval" parameter.

However, I'm unclear about a few implementation details:

How exactly is the heat flux imposed using the exchange method in QuantumATK?
Is the energy exchanged directly between predefined regions at every exchange interval step? How does this correspond to a physical heat flux value?
How should I define the size and location of the heat source and sink regions?
Should they be single layers of atoms, or should they span a certain number of unit cells?
How do I correctly choose the exchange interval?
What criteria should I consider when selecting the interval value to ensure physical accuracy and numerical stability?
How can I extract or calculate the actual heat flux value that is being applied during the simulation?
Is there a way to monitor the energy exchanged over time to derive the heat flux?

Any guidance would be greatly appreciated!

3

Scripts, Tutorials and Applications / Re: Assistance Required: Adding a New Potential and Moment Tensor Potential

« on: May 2, 2025, 16:45 »

Thanks again for the insights!
I now have a related question concerning energy convergence: How to resolve "Geometry optimization not converged. Stopped after 200 steps" during MD simulations of an amorphous bulk system?

I'm running a geometry optimization for a bulk material system in QuantumATK, but the calculation ends with the message:

"Geometry optimization not converged. Stopped after 200 steps."

I’d like to understand:

What are the main causes of this lack of convergence?

Should I increase the maximum number of optimization steps, or is this a sign of deeper issues like a poor initial structure or inappropriate force tolerance?

What are the recommended values for force tolerance, stress tolerance, and max step size in such cases?

Would refining the constraints block help?

Is it advisable to use a different optimizer (e.g., LBFGS vs. FIRE)?

Any tips, diagnostics, or example settings that worked for similar bulk systems would be appreciated

4

Scripts, Tutorials and Applications / Relationship behind the target temperature

« on: May 2, 2025, 16:30 »

How do simulation step size, heating rate, and time step collectively influence the target temperature in molecular dynamics simulations?
I'm trying to understand the underlying relationship between simulation step size, heating rate, and time step in molecular dynamics simulations.
My main confusion lies in how these parameters influence or determine the final (target) temperature, especially when it appears to be set "automatically" in some cases. Specifically:
Does the product of the heating rate and total number of time steps define the final temperature?
Is the target temperature always explicitly defined, or can it be implicitly set based on these parameters?
How should I properly balance the heating rate and time step to avoid unphysical temperature jumps or instability?

Any insight, including equations or examples from practical setups, would be greatly appreciated!

5

Scripts, Tutorials and Applications / Re: Assistance Required: Adding a New Potential and Moment Tensor Potential

« on: March 18, 2025, 08:29 »

"Greetings, as you mentioned, I have used the Tersoff potential to model my porous structure, where I aim to control its density by applying pressure. However, instead of reducing the density, I am observing an increase. What could be causing this issue, and could you suggest an effective workflow to achieve the desired lower density?"

6

Scripts, Tutorials and Applications / Re: Assistance Required: Adding a New Potential and Moment Tensor Potential

« on: February 11, 2025, 06:28 »

"Thanks for checking. If this functional form isn't directly supported, we might need to explore alternative SiO₂ potentials that QuantumATK can handle. Do you think we could approximate the third term using an existing potential or a combination of supported terms? Otherwise, we might need to consider a custom implementation or another workaround. Let me know your thoughts!"

7

Scripts, Tutorials and Applications / Assistance Required: Adding a New Potential and Moment Tensor Potential

« on: January 31, 2025, 11:53 »

Hello everyone,  I would like to know the detailed process for the following:

Adding New Potential from the Literature:
I have come across Vashishta potential in a publication (Ref: P. Vashishta, R.K. Kalia, J.P. Rino, and I. Ebbsjö (1990), "Interaction potential for SiO2: A molecular-dynamics study of structural correlations," Physical Review B, 41(17), 12197-12209. DOI: 10.1103/physrevb.41.12197), which is not a predefined potential set in quantumATK, that aligns well with my system's requirements. However, I am unsure of the exact steps needed to integrate it into QuantumATK even after referring this documentation. https://docs.quantumatk.com/tutorials/combining_potentials/combining_potentials.html
Could anyone please provide a detailed guide on the following aspects?

The required format or file type for custom potentials (e.g., parameter files or scripts).
The directory structure and location where such potentials should be placed.
Instructions for ensuring compatibility with the existing workflows, including any scripts or modules that need to be edited.
Any examples or templates that can serve as a reference for adding potentials from external sources.