Recent Posts

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21
You may need to go up to 100-300 k-points in the periodic direction to resolve artefacts related to the very specific band structure of graphene.
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You don't open the file itself, you select it in the Data View in NanoLab and then you can access the individual objects inside the file. For more assistance, you need to be more specific what exactly you do, with screenshots ideally.
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General Questions and Answers / Re: Connection to Cluster
« Last post by Anders Blom on November 4, 2025, 20:41 »
I think the warning message is quite clear, check your script for absolute paths to files that may not be available on the cluster in the same location. In general, always use relative paths to reference files you need from within a script that gets submitted to a different machine.
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I have yet to see a predefined ML model (we should not call them potentials) that can accurately predict DOS across many applications, but training a specific one for a given problem space is something we are working on.
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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.
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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.
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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?
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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.
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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.
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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
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