Recent Posts

41

General Questions and Answers / Re: DFT Phonon Transmission

« Last post by Anders Blom on November 4, 2025, 01:16 »

No, does not sound normal, I'd expect the whole thing to take a few minutes only, even on CPU. OK maybe an hour on CPU, as MACE is slow on CPU.

Maybe do a simple test calculation first on CPU for MoS2 with a similar number of atoms (make some distortion in the center to make it interesting) using the built-in ReaxFF potential in QuantumATK, just to get a feeling for the calculation time.

42

Future Releases / Machine Learning potential that can also predict density of state

« Last post by Lim changmin on November 3, 2025, 06:32 »

I understand that machine learning potentials have many advantages and are receiving a lot of attention. However, in the current version of ATK, the provided potentials can only compute force, stress, and energy. Meanwhile, several recent studies have shown the possibility of predicting the density of states (DOS) using machine learning. Therefore, it would be great if ATK could be updated to include ML potentials capable of calculating DOS as well.

43

General Questions and Answers / Re: DFT Phonon Transmission

« Last post by AsifShah on November 2, 2025, 09:18 »

Hi
I fine tuned MACE with additional data as per my requirement and when run on GPU, it is very very slow. It has been one day it shows only two progress cells in phonon transmission. The total size is 928 atoms

Is this normal?

44

General Questions and Answers / Re: Issue with launching simulation from SLURM

« Last post by filipr on October 31, 2025, 16:46 »

It's hard to help with this problem as there is not really enough information (what machines, OS, how was SLURM configured and how was the job submitted). Isuggest that you start by contacting your cluster admin and see if they can look into the issue, as it is most likely not a problem with QuantumATK but rather a problem with how the machines and SLURM was configured. The IT admin will be typically be able to log into the specific nodes and see whether the process is running and see if there is actually any output.

45

General Questions and Answers / Re: Parallelization issues with OrbitalMoment() in QuantumATK

« Last post by filipr on October 30, 2025, 16:03 »

Most QuantumATK operations do collective calls and cannot be manually mpi parallelized by e.g. just splitting a list of k-points among mpi processes.

What you can do instead is that you can first do the DFT ground state in a separate calculation and store the configuration to an HDF5 file. Then you can make a separate post-processing script that calculate OrbitalMoment() for a single k-point in a loop over a subset of all the k-points you are interested in, where the subset is determined from an input argument or environment variable (e.g. job array index).

Here's an unfinished example to give you the idea:

Code

import sys
my_process_index = int(sys.argv[1])
total_num_procs = ??

all_kpoints = numpy.array([[...], [...], ..., [...]])

my_kpoints = # logic to get local sequence of k-points here

configuration = nlread("dft_ground_state_calc.hdf5", BulkConfiguration)[-1]

orbital_moments = []
for kpoint in my_kpoints:
    orb_moment_analysis = OrbitalMoment(configuration, kpoints=MonkhorstPackGrid(1, 1, 1, k_point_shift=kpoint))
    orbital_moments.append(orb_moment_analysis.atomResolvedOrbitalMoment())

# Save 'orbital_moments' to file somehow, e.g. pickle

Then you can run this script either in a bash loop in a single script or submit it as multiple jobs or as a job array. Then you can collect the result files from each job and gather into a single array.

46

General Questions and Answers / Re: Question about Defect Diffusion Workflow Template

« Last post by pshinyeong on October 27, 2025, 09:34 »

Hello,

I have tried using the MACE potential for both vibrational correction and pre-relaxation. The results show that negative vibrational modes still appear for the hexagonal interstitial configuration, whereas the split interstitial defects do not exhibit any negative modes. Consequently, the diffusivity was only calculated for the split interstitial and split-interstitial–to–split-interstitial migration paths.

Also, regarding the NEB convergence issue you mentioned earlier — do you have any suggestions on how I can make the convergence faster? For reference, I used the PBE functional for generating the training data in the MTP-accelerated calculations (in the previous calculation).

Best regards,
Shinyeong

47

General Questions and Answers / Parallelization issues with OrbitalMoment() in QuantumATK

« Last post by corsicATK on October 25, 2025, 11:22 »

Hello everyone,

I need to calculate atom-resolved orbital moments using OrbitalMoment() in QuantumATK and obtain the values per atom and per k-point. My first question is: is it possible to directly get this information from the output?

If not, my fallback solution is to compute the function for a single k-point at a time and loop over all k-points. This works fine sequentially.

However, when I try to parallelize my code with mpi4py by distributing k-points over several ranks, I run into problems:

Deadlocks can occur during the computation.

At the end of the loop, all ranks return the same orbital moment values, even though each rank is supposed to work on a different k-point.

It seems that OrbitalMoment() does not execute independently on each rank and requires some form of internal synchronization or communication.

I would appreciate any guidance on:

Whether it is possible to obtain atom-resolved orbital moments for each k-point directly.

If independent parallel computation per k-point is possible, and how to do it safely with QuantumATK.

Thanks a lot for your help!

48

General Questions and Answers / Issue with launching simulation from SLURM

« Last post by AsifShah on October 21, 2025, 12:07 »

Dear Admin,
I am trying to launch a simulation from SLURM. It shows active status on squeue but the log file is empty for long time.
I m using latest QuantumATK X.2025.06.

Kindly help in this regard!

49

General Questions and Answers / Re: Recommended approach to generate an interface between two amorphous materials

« Last post by evansjc on October 20, 2025, 20:35 »

Hi Anders,

Great! I will try this. Thank you so much for your help!

50

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

« Last post by Priyadarshini 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!