Messages

1

General Questions and Answers / Question about non linear particle swarm optimization parameter

« on: November 19, 2025, 04:34 »

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.

2

General Questions and Answers / Issue on running MTP training simulation

« on: November 18, 2025, 06:52 »

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

3

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

« 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.

4

General Questions and Answers / Recommended Guideline for Creating a Ternary MTP by Combining Binary MTP

« on: September 16, 2025, 17:23 »

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.

5

General Questions and Answers / Approximating density and volume of unknown amorphous structure

« on: July 25, 2025, 05:42 »

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.

6

General Questions and Answers / hartree difference potential problem

« on: May 27, 2025, 08:32 »

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!

7

General Questions and Answers / can someone help with log file update problem?

« on: April 19, 2025, 17:22 »

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

8

General Questions and Answers / Langevin MD simulation friction variation

« on: April 9, 2025, 07:53 »

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.

9

General Questions and Answers / Re: Can we create MTP with dopant atom included?

« on: March 27, 2025, 15:11 »

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.

10

General Questions and Answers / Re: Can we create MTP with dopant atom included?

« on: March 17, 2025, 13:44 »

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

11

General Questions and Answers / Re: Can LCAO calculator srcipt be input in crystal structure prediction script?

« on: March 6, 2025, 20:24 »

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

12

General Questions and Answers / Can LCAO calculator srcipt be input in crystal structure prediction script?

« on: March 6, 2025, 20:02 »

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

13

General Questions and Answers / MTP force-field license problem and colum key duplicate error

« on: February 20, 2025, 05:38 »

Hello, I am trying to calculate GeTe MTP first based on the question in " https://forum.quantumatk.com/index.php?topic=12445.msg42955#new "

At first, the MTP training worked well, but after a few hours the error occurred
License Error: Unable to obtain a required license for the
requested license feature. It could mean there are no valid
licenses left, a problem with the connection to the license
server, or the license file does not contain the requested feature.
See below for more details.

Licensed number of users already reached.
Feature:       qatk_forcefield
License path:  [email protected]:
FlexNet Licensing error:-4,234

And I tried to recalculate it again and the other error occurred.

node01
Thu Feb 20 11:26:21 KST 2025
Traceback (most recent call last):
  File "/home/synopsys/quantumatk/W-2024.09/bin/../atkpython/bin/atkpython", line 8, in <module>
Traceback (most recent call last):
  File "/home/synopsys/quantumatk/W-2024.09/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 803, in __run_atkpython
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 803, in __run_atkpython
  File "gete_mtp.py", line 338, in <module>
  File "gete_mtp.py", line 338, in <module>
    training__set__table.addInstanceColumn(key='training_set', types=TrainingSet)
  File "zipdir/NL/ComputerScienceUtilities/Table/Columns.py", line 2269, in addInstanceColumn
    training__set__table.addInstanceColumn(key='training_set', types=TrainingSet)
  File "zipdir/NL/ComputerScienceUtilities/Table/Columns.py", line 2269, in addInstanceColumn
  File "zipdir/NL/ComputerScienceUtilities/Table/Columns.py", line 2301, in addColumn
NL.ComputerScienceUtilities.Exceptions.NLValueError: The column key, training_set, is already used in the table. Duplicate keys are not allowed.
  File "zipdir/NL/ComputerScienceUtilities/Table/Columns.py", line 2301, in addColumn
NL.ComputerScienceUtilities.Exceptions.NLValueError: The column key, training_set, is already used in the table. Duplicate keys are not allowed.
Traceback (most recent call last):
  File "/home/synopsys/quantumatk/W-2024.09/bin/../atkpython/bin/atkpython", line 8, in <module>
Abort(1) on node 3 (rank 3 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
Abort(1) on node 12 (rank 12 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 12
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 803, in __run_atkpython

I tried to find some answers to this "Duplicate keys are not allowed" error from atk forum but I couldn't find any.

Can anyone help me with this issue?

I attached the py file that I used bellow.

Thank you

14

General Questions and Answers / Re: Can we create MTP with dopant atom included?

« on: February 19, 2025, 20:43 »

Oh, and other question regarding to previous ones, if I were to investigate amorphous structure only, then can I skip step 1(crystal mtp) and go straight to step 2(amorphous mtp)?

15

General Questions and Answers / Re: Can we create MTP with dopant atom included?

« on: February 19, 2025, 07:45 »

Thank you for your reply.

Again, I have some other questions related to previous ones.

1. I want to train crystal GeTe with ratio 1:3 for Ge and Te each. However, from materials project, there was no Ge1Te3 crystal structures. So can I just use GeTe instead for MTP training to get Ge1Te3 MTP?

2. From your answer about putting C atom into GeTe, can I just use amorphous C doped GeTe with packmol as initial training set and skip step 1, 2(only getting GeTe MTP) ? I am little bit confused that why should I create only GeTe MTP first before training atom-doped GeTe.

Thank you