Messages

31

Scripts, Tutorials and Applications / Re: Fixing atoms during the optimization

« on: June 2, 2025, 15:09 »

Hi,

Looks right.

But out of curiosity, why would you keep W as fixed in WS2?

32

General Questions and Answers / Re: Which one would be the better placement option of Target Molecules for a FET ?

« on: June 2, 2025, 15:07 »

Hi,

If you place say O2 molecular around 2A above channel and optimize it, the DFT optimization will take care of whether there should be a bond or not between molecule and channel. Should give essentially same results in either case unless the molecule orientation matters.

33

General Questions and Answers / Re: Which one would be the better placement option of Target Molecules for a FET ?

« on: May 26, 2025, 14:04 »

Hi

I would suggest #1 and let the optimization determine where it will go.

34

General Questions and Answers / Re: Error while opening QATK in windows 11

« on: May 26, 2025, 09:13 »

Issue resolved. Turns out there were some quantumatk files from previous version. Had to uninstall and delete all Quantumatk files and reinstall.

35

General Questions and Answers / Error while opening QATK in windows 11

« on: May 23, 2025, 05:25 »

Dear admin,
How to resolve error?

I cant open ATK GUI on Windows 11 :

Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\Program Files\QuantumATK\QuantumATK-W-2024.09-SP1\bin\quantumatk.exe\__main__.py", line 7, in <module>
    sys.exit(start_quantumatk())
             ^^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers\__init__.py", line 811, in start_quantumatk
  File "zipdir\NL\__init__.py", line 10, in <module>
  File "zipdir\NL\GUI\Main\Main.py", line 207, in main
  File "zipdir\NL\GUI\Main\ApplicationManager.py", line 11, in <module>
  File "zipdir\NL\GUI\Preferences\Preferences.py", line 17, in <module>
  File "zipdir\NL\GUI\Tools\Builder\Stash\StashConstants.py", line 3, in <module>
  File "zipdir\NL\CommonConcepts\Configurations\BulkConfiguration.py", line 19, in <module>
  File "zipdir\NL\CommonConcepts\Configurations\AtomicConfiguration.py", line 13, in <module>
  File "zipdir\NL\Calculators\ExternalCalculators\ClassicalCalculators\PotentialBuilderUtilities.py", line 13, in <module>
  File "build/atkpython/Lib/site-packages/tremolox\TremoloXPotentialSet.py", line 19, in <module>
  File "build/atkpython/Lib/site-packages/tremolox\potentials\analyzer.py", line 42, in <module>
  File "build/atkpython/Lib/site-packages/tremolox\pymolo.py", line 8, in <module>
  File "build/atkpython/Lib/site-packages/tremolox\pymolo_avx.py", line 10, in <module>
ImportError: DLL load failed while importing _pymolo_avx: The specified procedure could not be found.

36

General Questions and Answers / Re: MPI error

« on: May 15, 2025, 18:49 »

Thanks. I will do the same.

37

General Questions and Answers / MPI error

« on: May 15, 2025, 11:04 »

Dear admin,

I got this error when running simulation on cluster on 3 nodes:

Abort(1615247) on node 0 (rank 0 in comm 0): Fatal error in PMPI_Init: Other MPI error, error stack:
MPIR_Init_thread(176)........:
MPID_Init(1525)..............:
MPIDI_OFI_mpi_init_hook(1597):
MPIDU_bc_table_create(320)...: Missing hostname or invalid host/port description in business card


SLURM Script:

#!/bin/bash

#SBATCH --job-name=QuantumATK
#SBATCH --ntasks=120
#SBATCH --ntasks-per-node=60
#SBATCH --nodes=2
#SBATCH --cpus-per-task=1
#SBATCH --output=%x-%j.out
#SBATCH --error=%x-%j.err
#SBATCH --partition=normal
#SBATCH --mem=210GB


cd $SLURM_SUBMIT_DIR
export ATK=/home/user/QATK/QATK_W_SP2/Install/quantumatk/W-2024.09-SP2/bin/atkpython
export MPI=/home/user/QATK/QATK_W_SP2/Install/quantumatk/W-2024.09-SP2/mpi/bin/mpiexec.hydra
export MPIE=/home/user/QATK/QATK_W_SP2/Install/quantumatk/W-2024.09-SP2/mpi/bin/mpiexec
export MKL_DYNAMIC=TRUE
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
export LM_LICENSE_FILE="####@*********":"###@***********"
export SNPSLMD_LICENSE_FILE="####@**********":"####@*******"

${MPI} -n 120 -ppn 60 ${ATK} in.py > out.log

38

General Questions and Answers / Re: ATK Error when running on cluster

« on: May 2, 2025, 12:44 »

Dear Anders Blom,

Please confirm if I am doing it rightly,
For cluster and single node:
export MKL_DYNAMIC=TRUE
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
When running on multiple cores on a cluster, I use: mpiexec.hydra -n 240 -ppn 60 atkpython input.py > output.log
When running on multiple cores on a single node, I use: mpiexec.hydra -n 60 atkpython input.py > output.log

For threads:
export MKL_DYNAMIC=TRUE
export OMP_NUM_THREADS=100
export MKL_NUM_THREADS=100
When running on multiple threads, I use: mpiexec -n 1 atkpython input.py > output.log

Am I doing the threading part correctly or there is any other way to speedup?
Best regards

39

General Questions and Answers / Re: ATK Error when running on cluster

« on: May 1, 2025, 08:19 »

Thanks for your response.
Will decreasing MPI and increasing threads decrease speed?

40

General Questions and Answers / ATK Error when running on cluster

« on: April 26, 2025, 11:39 »

Dear Admin,

I am running a 500+ atom geometry optimization on 240 cores (60 cores per node). After running for some time the simulation stopped giving error as:
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 175 PID 170903 RUNNING AT n3
=   KILLED BY SIGNAL: 9 (Killed)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 176 PID 170908 RUNNING AT n3
=   KILLED BY SIGNAL: 9 (Killed)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 177 PID 170910 RUNNING AT n3
=   KILLED BY SIGNAL: 9 (Killed)
===================================================================================


Could you please help how to resolve this issue as it requires me otherwise to run simulation again and again after sometime?

41

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

« on: March 19, 2025, 06:49 »

Dear Lim changmin,

If I am not mistaken,  I guess yes you can introduce many C atoms into your crystal structures. For instance, if your supercell has 20 atoms, you can do the following by creating new configurations as:
1. Replace some Ge with C in supercell
2. Replace some Te with C in supercell
3. Replace some Ge and Te with C in supercell

Depending on your accuracy then you can use all these configurations and do some active learning at high temperature with initial coefficients from your already generated MTP. For further accuracy you can then also do same on amorphous structures.

42

General Questions and Answers / Re: Help with Adding 𝐾 and 𝐾 ′ Points in BandStructure

« on: March 1, 2025, 14:47 »

Dear muhammadishaq,

Kindly use fatbandstructure in quantumatk instead of bandstructure.
Click on fatbandstructure and select project on spin.

43

Scripts, Tutorials and Applications / Re: ElectricFieldConstraint support for BaTiO3 structure

« on: January 6, 2025, 10:21 »

I faced somewhat similar issue with MoS2. Even under high electric field, the atoms barely move than expected. Just leaving this comment to follow-up on response from QATK.

44

General Questions and Answers / MLFF MTP for molecular and bulk configuration

« on: December 30, 2024, 17:13 »

Dear Admin,

I am training a MLFF for a system where I need to include both molecular and bulk configurations in training data.
However, in the end when trying to call rankFits() on MTP, it says error that molecular configurations have no stresses. Hence, does not find the best mtp among list of 30 mtps.

How to resolve this issue? and how to evaluate MTP in such case?

# Determine the best fit and extract its parameters.
 best_fit_index = mtp_training.rankFits(
 data_tags=None,
 weights=[[1, 1, 1], [1, 1, 1]],
 statistical_measure=R2Score
 )[0][0]


Thanks
best regards

45

General Questions and Answers / Interface MTP Training

« on: November 27, 2024, 23:03 »

Dear Admin,
Q1. I tried the code on "https://docs.quantumatk.com/manual/Types/CrystalInterfaceTrainingParameters/CrystalInterfaceTrainingParameters.html#NL.Study.MomentTensorPotential.CrystalInterfaceTraining.CrystalInterfaceTrainingParameters" for Iron/Copper interface but I get this error everytime. I tried changing random seed but still has same error. Kindly help resolve.

Master    : Handling exception in delegator process.
  Encountered TaskExecutionError: An exception was raised while executing task "a90b78e8ad0a11ef90b9801844e91328".
    Traceback (most recent call last):
      File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 1391, in __startParallelExecutionOnWorkerProcesses
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 1187, in _runTask
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 708, in run
      File "zipdir/NL/Study/MomentTensorPotential/FitMomentTensorPotential.py", line 464, in _execute
    NL.ComputerScienceUtilities.Exceptions.NLExecutionError: The training dataset contains no configurations. This error can probably be avoided by picking a different random seed.

Q2. Please answer the following. Step 1: I trained an MTP based with active learning of few configurations Step 2: I want to include more configurations so I combined reference data and active learning candidates from step 1 and passed onto Step 2. Step 3: I again want to include few more configurations. Now should I include all configurations from Step 1 and Step2 or only step 2? Also, in retaining should I change basis size as more configurations are being added or keep same for all Steps?