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

« Last post by Priyadarshini 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

General Questions and Answers / Issue with relaxation convergence in Charged Point Defect calculation

« Last post by leedongchan on January 19, 2026, 08:06 »

I am currently performing Charged Point Defect (CPD) calculations on Al-doped HfO2 supercells.

I have prepared optimized pristine cells for two compositions: Hf54Al10O123 (Hf-rich) and Hf32Al32O112 (Al-rich). While the calculation works fine for the Hf-rich composition, the relaxation for the Al-rich composition (Hf32Al32O112) fails to converge even after reaching 300 steps.

Here are the calculation details:

Calculator: GGA-PBESol

System Size: 176 atoms

K-point Sampling: 1x1x1

Electron Temperature (Broadening): 300 K

Optimization Settings: Max step length = 0.07 Å

Iteration Control Parameters:

Damping factor = 0.05

Number of history steps = 6

Effective rank fraction = 0.06

I have also verified that the forces are stable and do not fluctuate significantly when tested with 1x1x2 and 2x2x1 k-point grids.

Could you please provide any suggestions on how to resolve this convergence issue? Any help would be greatly appreciated.

Scripts, Tutorials and Applications / Re: MPI for QuantumATK-X-2025-06-SP1

« Last post by filipr on January 14, 2026, 11:44 »

The difference between v. U-2022.12 and X-2025.06 is probably that the former ships Intel MPI 2018.1 and the latter ships Intel MPI 2021.15. I am not sure what has changed between those versions in relation to PMI2, but according to Intels documentation (https://www.intel.com/content/www/us/en/docs/mpi-library/developer-guide-linux/2021-6/job-schedulers-support.html) it should support it. Maybe you need to manually set the path to the pmi library in the environment variable I_MPI_PMI_LIBRARY. You can also try srun with default/no arguments and see if it works out of the box.

If none of this helps, I suggest you ask Intel directly as we're not really in control nor knowledgeable about the inner workings of their MPI implementation. They have a user support forum here: https://community.intel.com/t5/Intel-MPI-Library/bd-p/oneapi-hpc-toolkit

Scripts, Tutorials and Applications / MPI for QuantumATK-X-2025-06-SP1

« Last post by hagelberg on January 6, 2026, 23:20 »

Hi - I'm trying to make QuantumATK-X-2025-06-SP1 functional on the ORNL cluster CADES.
While I was successful at installing the program, I haven't been able to run parallel jobs so far.
Here is an example for an MPI script that worked extremely well on CADES for QuantumATK-U-2022.12:

#!/bin/bash
#SBATCH --nodes 2
##SBATCH --ntasks-per-node 4
#SBATCH --exclusive
#SBATCH --mem=0
#SBATCH -p high_mem
#SBATCH -A cnms
#SBATCH -t 24:00:00
#SBATCH -o output_%j.out
#SBATCH -e output_%j.err

module purge
module load gcc/8

export SNPSLMD_LICENSE_FILE="[email protected]"

srun -N2 --ntasks-per-node=4 -v --mpi=pmi2 /home/fhagelberg/QuantumATK-2/QuantumATK-U-2022.12-SP1/atkpython/bin/atkpython /lustre/or-scratch/cades-birthright/fhagelberg/Olaf/zWS2+Hbridge-AFM-SGGA-Dojo-2-electrode.py

When I use the same script for QuantumATK-X-2025-06-SP1, cryptic error messages appear (see below). Pmi2 doesn't seem to work any longer (pmix is unavailable on CADES). Is there any other way I could implement MPI to run the program in a SLURM environment, leveraging srun which has turned to be very effective?

Error message:

srun: defined options
srun: -------------------- --------------------
srun: (null) : or-condo-c[317,364]
srun: jobid : 4348670
srun: job-name : atksub
srun: mpi : pmi2
srun: nodes : 2
srun: ntasks-per-node : 4
srun: oom-kill-step : 0
srun: verbose : 1
srun: -------------------- --------------------
srun: end of defined options
srun: jobid 4348670: nodes(2):`or-condo-c[317,364]', cpu counts: 36(x2)
srun: CpuBindType=(null type)
srun: launching StepId=4348670.0 on host or-condo-c317, 4 tasks: [0-3]
srun: launching StepId=4348670.0 on host or-condo-c364, 4 tasks: [4-7]
srun: topology/default: init: topology Default plugin loaded
srun: Node or-condo-c317, 4 tasks started
srun: Node or-condo-c364, 4 tasks started
slurmstepd: error: mpi/pmi2: value not properly terminated in client request
slurmstepd: error: mpi/pmi2: request not begin with 'cmd='
slurmstepd: error: mpi/pmi2: full request is: 00000000000000000000000000000000000000000000000

General Questions and Answers / Cannot visualize BlochState for Monolayer MoS2

« Last post by Angel Alonso on January 6, 2026, 22:40 »

Hello everyone,
I am interested in taking a look at the in-plane average of the Bloch's eigenfunction for specific (high symmetry) k points in a monolayer MoS2. Nevertheless, even though I included the Analysis tool "BlochState" after the LCAO Calculator, the BlochState objects in the Data view panel of the NanoLab interface would throw the error message "BlochState objects are not supported: SLMoS2_HSE06.hdf5" when double clicking on it. Right click and Open with editor would open the text file with the following content:

CUBE FILE. Bloch state (Bohr**(-3.0/2.0))
OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z
0 0.000000e+00 0.000000e+00 0.000000e+00
22 1.359581e-01-2.354864e-01 0.000000e+00
22 1.359581e-01 2.354864e-01 0.000000e+00
138 0.000000e+00 0.000000e+00 2.738734e-01

Export of CUBE files for complex grids is not yet supported.

It seems the BlochState is not properly output and stored. My current version of QATK is T-2022.03. Still, a colleague of mine ran the same calculation and tried to open BlochState on the latest version and failed to the same error. Could you help me solve this? Thanks in advance.

Details about calculation. Single hexagonal primitive unit cell of Monolayer MoS2, with out-of-plane crystal vector of length 20 Angstrom. HSE06 hybrid PBE functional, 9x9 k points for the in-plane sampling of Brillouin zone, and 65 H for the density mesh cutoff. I was particularly interested in the Bloch's eigenfunction at k=G, K, and M, for both Conduction and Valence bands (bands 13 and 12, respectively).

Installation and License Questions / max_force_threshold

« Last post by caliskan on December 27, 2025, 07:44 »

Hello,
My script involves:

method = NVEVelocityVerlet(
initial_velocity=ConfigurationVelocities(remove_center_of_mass_momentum=True),
max_force_threshold=10.0 * eV / Angstrom,
)

Here, "max_force_threshold=10.0 * eV / Angstrom," somehow, causes an error:

"NL.ComputerScienceUtilities.Exceptions.NLTypeError: The parameter, max_force_threshold, must be a PhysicalQuantity with units of eV/Ang."

I believe, it should normally work but it ends up with this error.

Thanks for your help in advance,

General Questions and Answers / Questions about mace trainingset

« Last post by Lim changmin on December 23, 2025, 18:57 »

Hi QuantumATK Support Team,

I’m following the QuantumATK MACE machine-learning tutorial, and I have a few questions about how the TrainingSet(s) used in the tutorial were prepared.

How was the “tutorial TrainingSet” generated?

The tutorial provides a pre-made TrainingSet file. From what I can tell, it looks like crystal random displacements (CRD) may have been used to generate structures.

However, I’m not sure whether the dataset was created via the MTP tutorial-style workflow (e.g., Step 1: “MomentTensorPotential training” / “reference calculator” to label energies/forces/stresses), or if a different workflow was used.

Also, was the TrainingSet created with “Recalculate training data = True” (i.e., structures generated first and then re-labeled with a specified reference calculator), or were the labels produced directly at the time the structures were generated?

Could you clarify the exact workflow and tools used to produce the provided TrainingSet?

How was the amorphous-only TrainingSet produced (and with what DFT settings)?

I noticed another TrainingSet that seems to contain only amorphous structures. Could you share how those amorphous configurations were generated?

Were they obtained from AIMD trajectories (e.g., melt–quench), or were they produced by geometry optimization from some initial amorphous guess (or another sampling method)?

For the DFT labeling step: what k-point sampling was used (Γ-only vs. Monkhorst–Pack, and the specific mesh if applicable)?

If AIMD was used: were the AIMD steps also run at Γ-only and then re-labeled later with a denser k-mesh, or were they labeled with the final k-point settings from the beginning?

Any details you can provide (e.g., whether stresses were included, exact k-point mesh, basis set / pseudopotentials, XC functional, and whether re-labeling was performed) would be very helpful so I can reproduce the tutorial dataset preparation reliably.

Thank you

General Questions and Answers / Regarding the directionality of the gate voltage

« Last post by zwh on December 23, 2025, 08:34 »

Dear Expert,

I would like to ask for your guidance on gate voltage settings in device simulations:

1. In single-gate devices, symmetric materials show nearly identical current whether the gate is on top or bottom. However, Janus materials show large differences depending on gate position. What causes this asymmetry?

2. For dual-gate devices with symmetric top and bottom gates, how are gate voltages set in the IV Characteristics module? When sweeping from 0 V to 1 V over 11 points, does 1 V mean both gates are biased at 1 V? If so, won’t the opposing electric fields cancel each other, reducing net field strength and weakening channel control?

Your insights would be greatly appreciated.

General Questions and Answers / Why device density of states is not opening to visualize the curve ?

« Last post by techenthusiast on December 19, 2025, 06:35 »

Dear experts,

Why device density of states is not opening to visualize the curve ? It is opening as editor where the data is written after execution.

General Questions and Answers / Showing Memory allocation error for one job task execution_Reg.

« Last post by techenthusiast on December 17, 2025, 10:08 »

Dear sir,

Good afternoon, Hope you are doing well. it is showing --Showing Memory allocation error for one job task execution_Reg..

The device structure is like - 4 Cylindrical GAA FET (2X2) . 4 Devices are having 4 different common dielectric (30) & 4 different metal gate.

How to resolve the issues?