Topics

1

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.

2

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

3

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?

4

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

5

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?

6

General Questions and Answers / Trying to install QATK W 2024

« on: October 21, 2024, 00:52 »

Dear Admin,

I upgraded my server OS from CentOS 7 to Ubuntu with following description:
Description:   Ubuntu 20.04.6 LTS
Release:   20.04
ldd (Ubuntu GLIBC 2.31-0ubuntu9.16) 2.31

And installed QATK_W version which was installed successfully as displayed in the message (attached pic).
However, the license servers still have CentOS7.

Then, I ran a py file which was created on QATK_2023_SP1 software. But ran into this error as below. Kindly help in this regard.

[SCL] Error:  FLEXlm version of the application is higher than the license daemon version. Please upgrade the license daemon to latest version (SCL-601)

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.

Cannot check out base license. SCL error message:
Version of vendor daemon is too old.
FlexNet Licensing error:-83,234

7

General Questions and Answers / Error in MoS2 forcefield implementation in QuantumATK

« on: October 7, 2024, 00:12 »

Dear Admin,

The actual MoS2 forcefield given in the original paper "https://www.frontiersin.org/journals/nanotechnology/articles/10.3389/fnano.2022.1034795/full#supplementary-material" is quite different from what is implemented in QuantumATK ReaxFF_CHOSMoNiAuTi_2022. Upon inspecting the implementation in QuantumATK against with original paper it, I found multiple lines have errors and one line is completely missing.

When using this forcefield it gives so many distortions in MoS2. Kindly, check into this or please let me know if I am missing anything.'

regards
Asif

8

General Questions and Answers / Charged vacancy in a device configuration for transmission

« on: October 3, 2024, 20:46 »

Dear Admin,

How to introduce charged vacancy in a device configuration for transmission?

9

General Questions and Answers / Setting different temperature for different regions

« on: August 16, 2024, 21:55 »

Dear Admin,

How can one set a heating rate only for a specific tag of atoms? In QuantumATK by default heating rate is set for all atoms.

10

General Questions and Answers / M3GNet error

« on: April 20, 2024, 21:21 »

Dear Admin,

When running M3GNet based molecular dynamics alongwith DZ3 correction as:

from tremolox.neighborlistcalculator.M3GNetCalculator import TremoloXM3GNetDirectPESCalculator
calculator_m3gnet = TremoloXM3GNetDirectPESCalculator(device='cpu')
calculator_d3 = TremoloXCalculator(parameters=DispersionD3Z(xc='PBE'))
calculator = CombinedCalculator([calculator_m3gnet,calculator_d3])

The simulations runs for sometime (few picoseconds) and then I get the following error:

TremoloXCalculator: Cart_create with procs 1 1 1 and periods 1 1 1 failed
Traceback (most recent call last):
  File "/home/Asif/QATK_V2023_12/quantumatk/V-2023.12/atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 780, in __run_atkpython
  File "VF_Multilayer_MoS2.py", line 406, in <module>
    md_trajectory = MolecularDynamics(
                    ^^^^^^^^^^^^^^^^^^
  File "zipdir/NL/Dynamics/MolecularDynamics/MolecularDynamics.py", line 1073, in MolecularDynamics
  File "zipdir/NL/Dynamics/MolecularDynamics/DynamicsEnergyForcesStress.py", line 30, in wrapped_analysis
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 46, in forcesFunction
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 72, in _checkAndUpdate
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 100, in _update
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 3080, in update
  File "zipdir/NL/Calculators/CombinedCalculator.py", line 373, in _update
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 3080, in update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/neighborlistcalculator/neighborlistcalculator.py", line 467, in _update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/TremoloBaseCalculator.py", line 501, in _update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 311, in __init__
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 251, in wrapper
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 540, in _setSystem
  File "build/atkpython/lib/python3.11/site-packages/tremolox/pymolo_avx.py", line 813, in conf_data_domain
tremolox.RuntimeError: SomeError: Error in file /slowfs/qatkdev2/users/qatktest/de02vlbamboo06/exlibs/.conan/data/tremolox/2023.08/quantumatk/stable/build/0bd0f4ede5a9e99cf053738a382952d716d95ea1/src/comm.cpp, line 234 (0): SomeError: StartParallel: Cart_create failed

Kindly help in this regard.

11

General Questions and Answers / Implementing a new Reactive Forcefield

« on: March 30, 2024, 03:40 »

Dear Admin,
I am trying to implement a new MoS2 reactive forcefield file into my simulation. The method I use is as follows:

1. I send the configuration to workflow and then choose the forcefield calculator. Then, I choose some inbuilt forcefield and add an optimization block.
2. Then send it to editor with all details present.
3. Then change reactive forcefield parameters with new parameters.

But it shows error. I have attached the python file and as well as the reactive forcefield parameter file. Kindly look into the matter why simulations shows error "Segmentation fault- core dumped"

Thanks
Regards

12

General Questions and Answers / M3GNet energies

« on: March 16, 2024, 08:08 »

Dear Admin,
When using M3GNet to calculate the total energy of a system the output shows nothing. Is it due to some bug?

Thanks
Here is the code:
# %% MoSe2

# Set up lattice
lattice = Hexagonal(3.288*Angstrom, 40.0*Angstrom)

# Define elements
elements = [Molybdenum, Selenium, Selenium]

# Define coordinates
fractional_coordinates = [[ 0.333333333333,  0.666666666667,  0.5           ],
                          [ 0.666666666667,  0.333333333333,  0.4583975     ],
                          [ 0.666666666667,  0.333333333333,  0.5416025     ]]

# Set up configuration
mose2 = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )
mose2_name = "mose2"


# %% Set LCAOCalculator

from tremolox.neighborlistcalculator.M3GNetCalculator import TremoloXM3GNetDirectPESCalculator
calculator = TremoloXM3GNetDirectPESCalculator(device='cpu')


# %% Set Calculator

mose2.setCalculator(calculator)

mose2.update()

nlsave('TE.hdf5', mose2)


# %% TotalEnergy

total_energy = TotalEnergy(
    configuration=mose2
)
nlsave('TE.hdf5', total_energy)

13

General Questions and Answers / Zero bias transmission

« on: March 5, 2024, 17:26 »

Dear Admin,
Does zero bias transmission include scattering across an interface with defect or it is ballistic?

If ballistic, why am I observing an increase of transmission in conduction and valence bands with defect at interface with respect to pristine interface?

14

General Questions and Answers / Query regarding GPU

« on: February 15, 2024, 09:35 »

Dear Admin,
We plan to perform QATK calculations on GPU.
Are there any particular GPU specifications we should consider for running QATK before buying one?

15

General Questions and Answers / Bug/Error in using MoS2 StillingerWeber2017

« on: February 9, 2024, 06:52 »

Dear Admin,

Please fix the bug/error when using StillingerWeber 2017:

Traceback (most recent call last):
  File "/home/user/QV/quantumatk/V-2023.09/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 900, in __run_atkpython
  File "StillWeber2017.py", line 588, in <module>
    optimized_configuration = OptimizeGeometry(
                              ^^^^^^^^^^^^^^^^^
  File "zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 611, in OptimizeGeometry
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 3069, in update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/TremoloBaseCalculator.py", line 499, in _update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 303, in __init__
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 246, in wrapper
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 421, in _setPotentials
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentialsets/potentialsetbase.py", line 424, in _register
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/potentials.py", line 1880, in _register
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/potentials.py", line 1870, in _convertValues
  File "build/atkpython/lib/python3.11/site-packages/tremolox/potentials/checks.py", line 144, in apply
TypeError: The parameter B = 84.0315436536 Ang**4 must have a unit that can be converted to Ang**5.0.


Paper: M. Wen, S. N. Shirodkar, P. Plechá?, E. Kaxiras, R. S. Elliott, and E. B. Tadmor, A force-matching Stillinger-Weber potential for MoS2: Parameterization and Fisher information theory based sensitivity analysis, Journal of Applied Physics, 122, p. 244301, 2017.

Thanks