Messages

31

General Questions and Answers / Re: Request for Feedback on Spin Transport System Setup

« on: June 20, 2025, 15:58 »

Hi,

Just my few cents:
If you are optimizing this configuration as bulk, you will need to add a vacuum in the z direction (to avoid spurious interaction between Ni and Au) and keep either electrodes (say Ni) outer layer fixed to emulate bulk behavior. At the same time, you need to keep the gold outer layer rigid (or fixed in xy direction) so that it can move in the z direction to avoid any internal stresses during optimization. This way, you can optimize the structure.
Also, make sure the gold and nickel are optimized from the bulk unit cell before forming the interface. Also, choose a low-strain interface from Interface Builder (though it depends on computational complexity).

Also, I wanna know if initial spin has any effect on the final optimized configuration or just helps in quick optimization?

32

General Questions and Answers / GPU QATK

« on: June 19, 2025, 03:31 »

Dear Admin,

I recently installed the X-2025.06 version of QuantumATK, which supports GPU acceleration for DFT calculations.
In the bin folder, I found the following files:
atkpython
atkpython_gpu
atkpython_system-mpi
quantumatk

In the mpi/bin, I found the following files:
cpuinfo
hydra_bstrap_proxy
hydra_nameserver
hydra_pmi_proxy
impi_info
mpiexec
mpiexec.hydra

Kindly let me know if this is how to run DFT simulations on GPU:

atkpython_gpu input.py > output.log

or

mpiexec.hydra -n 2 atkpython_gpu input.py > output.log (2 here for using 2 GPUs on a given node)
My GPU node shows 6 GPU machines when using nvidia-smi command.

If I am doing it incorrectly, kindly help me do it properly for single-GPU and multiple-GPU machines on a given node.

Also, do we require any licenses to use GPU acceleration because I tried atkpython_gpu input.py > output.log and it shows:
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.
No such feature exists.
Feature:       qatk_gpu
License path:  [email protected]:
FlexNet Licensing error:-5,234

33

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

« on: June 4, 2025, 18:24 »

Sadly no. I deleted them all

34

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

« on: June 2, 2025, 15:18 »

Dear Anders Blom,

The older version was from 2023.
The files that were causing trouble were in the path: C:\Users\Lenovo\.quantumatk
It was the .quantumatk folder that was causing the trouble.

Yes, there was a popup just after I double clicked the QuantumATK icon.

35

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?

36

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.

37

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.

38

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.

39

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.

40

General Questions and Answers / Re: MPI error

« on: May 15, 2025, 18:49 »

Thanks. I will do the same.

41

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

42

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

43

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?

44

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?

45

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.