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Messages - Lim changmin

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1
General Questions and Answers / Questions about mace trainingset
« 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

2
Hi, a few days ago, I posted some questions about MTP error(https://forum.quantumatk.com/index.php?topic=13336.0). From the reply, I tried to study MACE training potential, but didn't work out due to the fact that I didn't have GPU. So I returned to the MTP training, but an error occurred that I have never encountered.

This time the job terminates with many repeated warnings about the Study HDF5 file not existing, and then crashes with an HDF5 “truncated file” error leading to MPI_Abort.
UserWarning: The original file of the Study object 'GeTeCN_amor_train_gga.hdf5' no longer exists.
This means no task results will be saved to the new file.

During MTP training update / dataset construction, the run fails while reading an HDF5 file:

OSError: Unable to open file (truncated file: eof = 338986776, sblock->base_addr = 0, stored_eoa = 338986929)
  File "zipdir/sergio/HDF5/HDF5.py", line 111, in __init__
  File "/home/synopsys/quantumatk/X-2025.06/atkpython/lib/python3.11/site-packages/h5py/_hl/files.py", line 567, in __init__
OSError: Unable to open file (truncated file: eof = 338986776, sblock->base_addr = 0, stored_eoa = 338986929)
OSError: Unable to open file (truncated file: eof = 338986776, sblock->base_addr = 0, stored_eoa = 338986929)
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/synopsys/quantumatk/X-2025.06/atkpython/lib/python3.11/site-packages/h5py/_hl/files.py", line 231, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
I attached the rest of the error script below file.

So here's the question
1. What exactly triggers the repeated warning:
“The original file of the Study object … no longer exists”?
Is this typically caused by launching the run from a temporary working directory (e.g., scratch/zipdir) where the original Study HDF5 is not available?
Is there a recommended way to set an absolute/persistent output path for the Study/Workflow files in Active Learning?

2. Regarding the fatal error:
HDF5 truncated file
Is this usually due to interrupted I/O (walltime kill, quota/full filesystem, network filesystem instability), or can concurrent MPI access to the same HDF5 also corrupt/truncate it?
In Active Learning MTP, which specific HDF5 file is being read at this stage (the Study file, a workflow state file, training dataset file, or something else)? Any tips to identify it deterministically?

3. What is the recommended restart/recovery procedure after an HDF5 truncation?
Should I delete/rename the corrupted HDF5 and restart from the last valid iteration?
Is there an official method to validate/repair the HDF5 (or is rollback the only safe option)?

I also attached slurm file and py file that I used

Thank you

3
Thank you for the advice. I'll try it.

4
Hello,
I am trying to use the NonLinearParticleSwarmOptimizationParameters (NLPSOP) for testing purposes. In the TiSi MTP tutorial, it is mentioned that NLPSOP can define the MTP more accurately, so I wanted to try it in my training script. I attached the NLPSOP settings I used as Figure 1.

However, when I run the script, I get the following error:

AttributeError: 'NonLinearParticleSwarmOptimizationParameters' object has no attribute 'initialCoefficients'. Did you mean: 'initialCoefficientsFromFile'?

Could you please let me know how to properly use NLPSOP when training an MTP? In particular, I would like to know:
1. How to correctly specify the NLPSOP block in the training script, and
2. How to set and use initialCoefficientsFromFile (e.g., what kind of file is expected and how to generate it).

Thank you in advance for your help.

5
Hello, I am trying to train MTP with GeTe doped with C and N.
However, I have encountered an error that I have never seen.
This is the error script below.

node01
Tue Nov 18 10:59:59 KST 2025
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error: *** JOB 4041 ON node01 CANCELLED AT 2025-11-18T11:05:56 ***
slurmstepd: error: *** STEP 4041.0 ON node01 CANCELLED AT 2025-11-18T11:05:56 ***

I don't know why the hdf5 no longer exist.
Can anyone help me to solve the error?

Thank you.
I have also attached a py file that I used

6
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.

7
Hello everyone,

I am seeking guidance on the recommended workflow for developing a Moment Tensor Potential (MTP) for the amorphous Ge-Se-Te ternary system.

A key challenge is the lack of existing DFT or experimental data for the amorphous ternary phase, which makes direct training and validation difficult. To address this, I have formulated a bottom-up strategy which involves creating and validating the constituent binary potentials first:

1. Develop and validate a Ge-Te MTP against published research.

2. Develop and validate a Ge-Se MTP against published research.

3. Develop and validate an Se-Te MTP.

4. Finally, combine these three validated binary MTPs to describe the full ternary system.

My underlying hypothesis is that if a combined potential accurately reproduces the structural properties (e.g., RDF, CN, angular distribution) of the constituent binary systems, it will also provide a reliable description of the ternary system. I have already successfully developed the Ge-Te and Ge-Se potentials, and their results show excellent agreement with previous studies.

With the recent release of QuantumATK X-2025.06, I noticed several improvements to MTP training, including a new 'Load mtp file' block and the ability to save the fit in an MTPParameters object.

This leads to my main questions:

1. Is my proposed methodology—developing and then combining three separate binary MTPs—a scientifically valid and recommended approach for creating a potential for a ternary system like this?

2. Does QuantumATK 2025.06 provide a specific tool or a recommended workflow (perhaps using the new features mentioned above) to combine these separately trained MTPs into a single, functional potential for the Ge-Se-Te system?

Thank you in advance for your support and insights.

8
Hello,

I am currently preparing to perform molecular dynamics simulations on an amorphous Ge-Se-Te structure. As a preliminary step, I plan to generate an initial amorphous configuration using Packmol. However, due to the lack of experimental data for the GeSeTe system, I am unable to determine a reliable reference density.

Is there a recommended approach to theoretically estimate the density of such a structure in the absence of experimental measurements?

Thank you in advance.

9
Hello,

I'm currently trying to calculate the Hartree difference potential (HDP) for a silicide/silicon contact and visualize it alongside the projected local density of states (PLDOS), as shown in the QuantumATK tutorial here:
https://docs.quantumatk.com/tutorials/ag_si_interface/ag_si_interface.html

However, the HDP results I obtained are not what I expected. I assumed that the HDP would show a peak near the interface and then gradually decrease, clearly indicating the Schottky barrier height. But the resulting graph looks quite different from this expectation.

For reference, I used silicon region lengths of 70 Å and 100 Å in separate calculations. I also attached the structure file that I used

Could anyone help me understand why the HDP results might appear unusual or inconsistent with expectations?

Thank you in advance for your help!

10
Hello, I am trying to optimize some amorphous structures, but the log file would not update.
I am not sure what caused this issue.
I am attaching the log file

the log file won't update and so as hdf5 file

It just stopped at this point
+------------------------------------------------------------------------------+
| Diagonalization solver parallelization report                                |
+------------------------------------------------------------------------------+
| Total number of processes: 240                                               |
| Total number of k-points: 14                                                 |
| Processes per k-point: 18                                                    |
+------------------------------------------------------------------------------+
| Process occupation                                                           |
+------------------------------------------------------------------------------+
| Processes   0 -  17: |=====================================================| |
| Processes  18 -  35: |==========================                           | |
| Processes  36 -  53: |==========================                           | |
| Processes  54 -  71: |==========================                           | |
| Processes  72 -  89: |==========================                           | |
| Processes  90 - 107: |==========================                           | |
| Processes 108 - 125: |==========================                           | |
| Processes 126 - 143: |==========================                           | |
| Processes 144 - 161: |==========================                           | |
| Processes 162 - 179: |==========================                           | |
| Processes 180 - 197: |==========================                           | |
| Processes 198 - 215: |==========================                           | |
| Processes 216 - 233: |==========================                           | |
| Processes 234 - 239: |                                                     | |
+------------------------------------------------------------------------------+
| WARNING: Some processes are idle.                                            |
+------------------------------------------------------------------------------+
|   0 E = -840.065 dE =  1.374980e+01 dH =  1.790209e+00                       |

thank you

11
Hello,

I'm currently performing melt-quench molecular dynamics simulations to generate amorphous structures using the Langevin thermostat. In the Langevin method, there's a friction parameter (with a default value of 0.01).

When I use the default value, the system's temperature rapidly rises to unphysically high values like 1e12 K or 1e11 K. However, when I increase the friction coefficient to 0.05 or 0.1, the temperature starts to fluctuate reasonably well around the reservoir temperature.

Still, for some structures, the temperature control is not stable enough. So I'm considering increasing the friction coefficient further to 0.15 or even 0.2.

Here are my questions:

Would increasing the friction coefficient to this extent affect the resulting amorphous structure?

From a theoretical standpoint, how much can I increase the friction coefficient before it starts to significantly affect the dynamics and structural outcomes? Is there a practical or theoretical upper limit?

Kindly waiting for the response.

12
Thank you for your response.

I am currently working on training an MTP exclusively for amorphous structures, as there is no corresponding crystalline phase.

I have some questions regarding Step 1 of the standard crystalline training protocol. For training amorphous structures, active learning requires both MTP training and a training set generation function. In this process, MTP training is typically initialized using the random displacement function applied to a crystalline structure.

My question is: Can the crystal random displacement function be used for amorphous structures as well? Or is it strictly applicable to crystalline phases?

I am asking because, in the tutorial (https://docs.quantumatk.com/tutorials/mtp_hfo2/mtp_hfo2.html), the workflow in Step 1 explicitly refers to the "bulk phase." I am a bit confused by the term "crystal" in "crystal training random displacement function" and whether it applies to amorphous systems.

I would appreciate any clarification on this.

13
Dear Anders Blom,

Thank you for your kind response.

I have successfully created the GeTe MTP and am now working on incorporating carbon atoms into the GeTe structure using the "defect training set" or "defect formation set".

However, as far as I understand, both methods seem to allow the introduction of only a single interstitial atom. I may be mistaken, but I wanted to check if there is a way to modify this feature to accommodate multiple interstitial atoms.

My goal is to introduce at least three carbon atoms into the GeTe structure. Would it be possible to modify the "Defect" feature to accommodate multiple interstitial atoms? Alternatively, would you advise modifying the atomic coordinates directly in the script?

I would greatly appreciate any guidance you could provide on this matter.

Thank you for your time and assistance.

Best regards,
Changmin

14
Also, I have additional question

I attempted to create an MTP (Machine Learning Interatomic Potential) for GeTe that could be applied to structures with different Ge and Te ratios.

For the ML-FF (Machine Learning Force Field) crystal training, I only used GeTe structures with a 1:1 ratio, as no other compositions were available.

However, for the ML-FF amorphous training, I generated amorphous GeTe structures using Packmol with varying Ge:Te ratios, including 1:1, 1:4, and 23:77, among others.

My question is:
Since I only used 1:1 ratio GeTe for crystal training, while incorporating various Ge:Te ratios for amorphous training, can the resulting MTP still be considered reliable?

I am currently validating the MTP, and the fitted results seem reasonable(figure posted). However, I am still uncertain whether the difference in training data composition could affect the generalization and accuracy of the MTP.

Would this discrepancy impact the reliability of my potential?
Thank you

15
Dear all

Hello, I am trying to make MTP for Carbon-doped Ge(n)Te(m) (n,m are integers).
To start MTP, the tutorial for TiSi MTP indicate to use crystal structure first and then train amorphous.
For amorphous, We can make these structures with packmol, however for crystals, we cannot find structures with C, Te, Ge included.

Therefore I am trying to use crystal structure prediction(i.e. csp). From tutorial, it used forcefield calculator, but I want to use LCAO for more accuracy.
But LCAO requires bulk configuration defined first.
And the script in csp only show elements and the calculator script is prior to elements.
Can someone help me how to revise LCAO for csp?

Thank you

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