Messages

1

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

« 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

2

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

« on: September 26, 2025, 11:11 »

Hello ,

I re-ran the calculation with the corrections previously suggested:

Added the chemical potential calculation for the boron atom

Tightened the convergence criteria in the calculator

Linked the calculators as described in the PDF

Despite these changes, the job crashed near the end with the following error:

Code

1_Defect_Diffusion_Workflow/1_Trial_1/250921_003210_4ibppi7p.hdf5' no longer exists.This means no task results will be saved to the new file.
Traceback (most recent call last):
  File "/home/synopsys/quantumatk/X-2025.06/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 912, in __run_atkpython
  File "./defect_diffusion_MTP_results.py", line 901, in <module>
    filter_migration_pairs_based_on_prerelaxation_calculator_barrier_heights(
  File "./defect_diffusion_MTP_results.py", line 895, in filter_migration_pairs_based_on_prerelaxation_calculator_barrier_heights
    filtered_defect_migration_pairs_table.append(defect_pair_table[index])
  File "zipdir/sergio/HDF5/Table.py", line 2476, in append
  File "zipdir/sergio/HDF5/Table.py", line 1633, in validate
ValueError: The initial_defect column can only contain instances of NamedPointDefect, was list
Abort(1) on node 20 (rank 20 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20

I’ve attached the link to the relevant output files for your review through message, please alert me if the message was not sent because I have sent the message twice but it didn't show up in the sent box.

Could you please check where my setup or workflow may be incorrect, particularly around the initial_defect field expected to be a NamedPointDefect? Any guidance on resolving this would be appreciated.

Also, this run took a little over three days on 5 nodes (48 cores per node; tasks per node: 6; CPUs per task:; 8 ) before failing. Is this runtime typical for the Defect Diffusion workflow with these settings, or does it suggest a misconfiguration or inefficiency?

Thank you in advance for your help.

3

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

« on: September 14, 2025, 07:42 »

I also tried this using LCAO calculator for all 4 calculator but still gave me error

Code

zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object '/home/edrl_01/Desktop/1_Diffusion/a_MTP/2_SiB_Defect_Diffusion/2_Trial_2_canceled/2_Trial_2/250912_215415_i1dbrf1h.hdf5' no longer exists.This means no task results will be saved to the new file.
Traceback (most recent call last):
  File "/home/synopsys/quantumatk/X-2025.06/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 912, in __run_atkpython
Traceback (most recent call last):
  File "/home/synopsys/quantumatk/X-2025.06/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 912, in __run_atkpython
  File "./defect_diffusion_results.py", line 714, in <module>
    neb_table = generate_nebs_from_defect_migration_paths(
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "./defect_diffusion_results.py", line 695, in generate_nebs_from_defect_migration_paths
  File "./defect_diffusion_results.py", line 714, in <module>
    nebs = defect_migration_paths.generateNEBs(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "zipdir/NL/Defects/Migration/DefectMigrationPaths.py", line 538, in generateNEBs
    neb_table = generate_nebs_from_defect_migration_paths(
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "./defect_diffusion_results.py", line 695, in generate_nebs_from_defect_migration_paths
    nebs = defect_migration_paths.generateNEBs(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "zipdir/NL/Defects/Migration/DefectMigrationPaths.py", line 538, in generateNEBs
  File "zipdir/NL/Dynamics/Optimization/NudgedElasticBand.py", line 248, in __init__
  File "zipdir/NL/Dynamics/Optimization/NudgedElasticBand.py", line 248, in __init__
  File "zipdir/NL/CommonConcepts/QuantityChecks.py", line 764, in checkAndSetConfigurationList
  File "zipdir/NL/CommonConcepts/QuantityChecks.py", line 764, in checkAndSetConfigurationList
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 2480, in _compare
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 2480, in _compare
NL.ComputerScienceUtilities.Exceptions.NLValueError: The configurations in a NudgedElasticBand are only allowed to differ in the position of the atoms and the cell vectors.
Configuration 1 differs from configuration 0:
The tags of the atoms differ in the compared configurations.
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
NL.ComputerScienceUtilities.Exceptions.NLValueError: The configurations in a NudgedElasticBand are only allowed to differ in the position of the atoms and the cell vectors.
Configuration 1 differs from configuration 0:
The tags of the atoms differ in the compared configurations.
Abort(1) on node 16 (rank 16 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 16

Any help would be appreciated. Thanks

4

General Questions and Answers / Question about Defect Diffusion Workflow Template

« on: September 10, 2025, 07:16 »

Hello,

I am trying to use the Defect Diffusion workflow template to calculate the dopant diffusion rate in silicon, and I have a few questions about the setup.

I created an MTP using defect training and used that potential for pre-optimization, phonon calculation, and the LCAO calculator for bandgap and reference calculations. I also added an Element Reference Material block for the dopant chemical potential calculation. Since there is no tutorial available for this workflow template, I am not sure if this setup is correct.

The calculation finished successfully and a diffusion rate result was generated. However, when I click on it, the results table appears empty.
Has anyone experienced this issue before or could provide some guidance on how to resolve it?

Thank you in advance!

5

General Questions and Answers / Problem running QuantumATK X-2025.06 in parallel with SLURM

« on: August 31, 2025, 08:49 »

Hi,

I just updated to QuantumATK X-2025.06.
On the main node, atkpython runs fine.
But when I try a parallel job with SLURM, it stops immediately and no log file is created.
With the previous version of QuantumATK, the same job script worked for parallel calculation.

I attached my job script and the slurm out file.
Any ideas what changed in this version or how to fix MPI parallel runs?

Thank you

6

General Questions and Answers / how to restart Defect MTP Training after interruption

« on: August 18, 2025, 05:36 »

Hello everyone,

I started defect MTP training using the workflow template, but the calculation took more than three days, so I had to stop it manually. Is there a way to restart the training from where it left off, or do I need to start over from the beginning?

Thanks in advance for your help!

7

General Questions and Answers / How to Handle Non-Orth. Axes in NEGF Calculations for Monoclinic structure

« on: April 28, 2025, 05:41 »

In NEGF calculations, the C direction is always considered the transport direction, and transmission can only be calculated when the A and B directions are orthogonal to C in the unit cell. However, for a monoclinic structure, no matter how I cleave it, the A and B directions are never orthogonal to C.
My current approach is to cleave the surface first, add vacuum along the C direction (above and below the surface), perform structure optimization only on the surface layers, and then switch the B and C directions for the transmission calculation.
However, even after doing this, the C (formerly B) direction is still not orthogonal to the other axes.
How can I solve this issue?

8

General Questions and Answers / Re: How to Resolve reservoir temperature Showing 0K in NVT NoserhooverMD Simulation?

« on: February 25, 2025, 08:10 »

This output wasn't from the original question but I encountered this problem again in other calculation so I'm posting that input file and the screenshots.

9

General Questions and Answers / How to Resolve reservoir temperature Showing 0K in NVT NoserhooverMD Simulation?

« on: January 19, 2025, 08:53 »

Hello,

I am using the constant-density melt-quench template to create an amorphous structure. However, starting from the second MD step (NVT Nose-Hoover), the reservoir temperature is fixed at 0 K, even though I set it to range from 3000 K to 1100 K.

Is this an error in the setup, or could it be a problem with the Nose-Hoover thermostat configuration?

Thank you for your help!

10

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

« on: January 19, 2025, 07:28 »

Hello, I am working on the same thing and I have some questions regarding MTP with dopant atom

1. In step 4, you mentioned repeating active learning for a-GeTe with carbon included. Can I skip creating a base MTP with carbon and go directly to active learning after step 3?

2. Before Creating C-doped a-GeTe in step 3, I should use the MTP trained from Step 2 to create amorphous GeTe using Melt Quench method for more accurate a-GeTe?

3. Is it possible to use the defect training protocol with carbon as an interstitial or substitutional dopant in step 1 to skip step 3 altogether?



Thank you in advance for your guidance!

11

General Questions and Answers / Log file won't update

« on: January 16, 2025, 17:11 »

Hello,

When I try to do MD calculation based on Melt Quench template in the workflow, the log file won't update at some point and calculation doesn't finish. I attached the calculation file if anyone wants to reproduce the same error. (I couldn't upload the log file for some reason even though it's only 3.7mb) Also, the log file finished with 'geometry optimization converged in 140 steps' but calculation didn't finish and also there is no optimized configuration.

Can anyone help me understand why this happens? Thanks

12

General Questions and Answers / difference between optimization using device LCAO and LCAO for bulk

« on: January 10, 2025, 06:02 »

Hello,

I have a question about the best approach for relaxing a device/bulk configuration. Specifically, my system is a vacuum/metal (6 layers)/barrier (6 layers)/metal (6 layers)/vacuum structure. I want to optimize only two layers on each side of the interfaces (i.e., four layers total at each interface) while keeping the other layers fixed.

My ultimate goal is to calculate transmission, so eventually I need to convert this bulk configuration into a device configuration. However, I noticed that:

Before optimization, I can convert the bulk configuration into a device configuration without any issues.
After optimization, the optimized configuration cannot be converted into a device configuration.
Given this, I have two questions:

Is it more reasonable to create the device configuration first and then optimize it (using a Device LCAO Calculator), rather than optimizing the bulk configuration and then converting it into a device configuration?

Is there any difference between these two methods in terms of results or best practices?

Any guidance would be greatly appreciated. Thank you!

13

General Questions and Answers / Removing Vacuum from Interface Structure and creating symmetrical interface

« on: November 27, 2024, 09:27 »

Hello,

I've created a Co/CoTi interface structure, as shown in the attached image. In this structure, two layers near the interface are relaxed, and there is a 10Å vacuum on both sides. Now, I want to construct a Co/CoTi/Co interface where CoTi/Co interface remains identical to the existing Co/CoTi interface to avoid repeating the relaxation process (as the structure contains many atoms). Additionally, I need to remove the vacuum regions to prepare the structure for a device configuration.

Is there an efficient way or a specific Builder tool in QuantumATK to
1. Remove the vacuum from the existing structure?
2. Create a symmetrical Co/CoTi/Co interface based on the relaxed Co/CoTi interface?

For clarity, I've included a second image to illustrate the structure I'm aiming to build. Thank you in advance for your guidance!

14

Installation and License Questions / Re: Cannot assign more than 5 cores for AKMC

« on: October 23, 2024, 06:08 »

Yes, threading solved the issue. Thank you!

15

General Questions and Answers / Re: configuration for Training set created by random displacement parameters

« on: October 23, 2024, 06:07 »

Thank you for your response.

After running the Defect Training Workflow, I was unable to locate any file containing the Training Set. However, I do have the 'mtp' object, which I can open in the Movie Tool. In my case, two defect configurations were generated by the defect block, and I used a sample size of 10, 20, and 10 for Rattle Atom, Rattle Cell, and Rattle Volume parameters, respectively.

I am curious about the resulting trajectory, as it consists of 140 steps, whereas I was expecting 80 steps (40 configurations per defect). Could you help clarify why this might be the case?

Thank you for your assistance.