Topics

1

Scripts, Tutorials and Applications / Connection to server lost during the execution

« on: January 19, 2026, 08:26 »

Hello quantumATKteam, I am experiencing a server connection issue in QuantumATK that occurs during execution and not at the submission stage. The job submits successfully and begins running, but during runtime it terminates with the error message “connection lost after 5 heartbeats”. The behavior is inconsistent: in some cases the calculation ran for about 12–15 days, in another case for around 10 days, and once it was cancelled within a single day, all failing with the same heartbeat connection error. This indicates that the server disconnects unpredictably while the simulation is actively executing. I have tried restarting QuantumATK and the system, reconnecting or re-adding the server in the Job Manager, and checking license and network status, but the issue persists. I would appreciate any suggestions regarding possible causes such as heartbeat timeout settings, long-runtime stability, network interruptions, license heartbeat limits, or resource constraints during extended QuantumATK calculations. Below I have pasted the lines printed on the log.
|--------------------------------------------------|
Calculating Eigenvalues    : [Sat Jan  3 10:16:40 2026]: Connection to server lost - reconnection attempt 2/5.
[Sat Jan  3 10:16:40 2026]: Connection to server lost - reconnection attempt 2/5.
============[Sat Jan  3 10:18:46 2026]: Connection to server lost - reconnection attempt 3/5.
[Sat Jan  3 10:18:46 2026]: Connection to server lost - reconnection attempt 3/5.
======[Sat Jan  3 10:20:46 2026]: Connection to server lost - reconnection attempt 4/5.
[Sat Jan  3 10:20:46 2026]: Connection to server lost - reconnection attempt 4/5.
=======[Sat Jan  3 10:22:46 2026]: Connection to server terminated after failing 5 heartbeats



|--------------------------------------------------|
Calculating Eigenvalues    : ===============================[Fri Jan 16 03:24:26 2026]: Connection to server terminated after failing 5 heartbeats

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 / 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!

4

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.