Messages

1

General Questions and Answers / Re: DFT Phonon Transmission

« on: November 2, 2025, 09:18 »

Hi
I fine tuned MACE with additional data as per my requirement and when run on GPU, it is very very slow. It has been one day it shows only two progress cells in phonon transmission. The total size is 928 atoms

Is this normal?

2

General Questions and Answers / Issue with launching simulation from SLURM

« on: October 21, 2025, 12:07 »

Dear Admin,
I am trying to launch a simulation from SLURM. It shows active status on squeue but the log file is empty for long time.
I m using latest QuantumATK X.2025.06.

Kindly help in this regard!

3

General Questions and Answers / Re: Unexpected Transmission Channel in Monolayer Graphene DFT Transport CalculationD

« on: October 13, 2025, 14:11 »

Hi kaihuang,

Can you check with these quick fixes for the file D0_BulkDevice.py

1. Increase electrode extension.
2. Use k_point_sampling = MonkhorstPackGrid(na=12, nc=300).
3. Use medium basis set.

4

General Questions and Answers / Re: DFT Phonon Transmission

« on: September 3, 2025, 20:03 »

Thanks. I will take a look into universal forcefields.

5

General Questions and Answers / Re: RAMAN Spectrum on monolayer MoS2

« on: September 3, 2025, 19:43 »

Ah, just follow up. It turned out I had to choose the polarization average rather than polarization in/out. That worked, qualitatively atleast.

6

General Questions and Answers / Re: Executed IV HDF5 File is not showing at "Data" Section even saved at the folder

« on: September 1, 2025, 07:26 »

Hi,

Try closing and reopening QuantumATK. Also, make sure you have selected right folder under project icon (Top left)

7

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

« on: August 31, 2025, 18:09 »

Hi Pshinyeong,
From what I see you have commented the following lines:
#mpirun ~/QuantumATK23/quantumatk/V-2023.09/bin/atkpython_system-mpi $PYTHON_SCRIPT > $LOG_FILE
#mpirun /home/edrl_05/QuantumATK/QuantumATK-U-2022.12-SP1/bin/atkpython $PYTHON_SCRIPT > $LOG_FILE

Also, instead of using mpirun, I would recommend using QATK inbuilt mpiexec.hydra for parallelization and atkpython for execution.
Also, you need to update the paths, so your SLURM script will look something like this:

Code

#!/bin/bash

#SBATCH --job-name=QuantumATK
#SBATCH --ntasks=60
#SBATCH --ntasks-per-node=60
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --output=%x-%j.out
#SBATCH --error=%x-%j.err
#SBATCH --partition=normal
#SBATCH --mem=210GB
#SBATCH --nodelist=n16,n15,n14

cd $SLURM_SUBMIT_DIR
export ATK=/home/edrl_05/QuantumATK/quantumatk/X-2025.06/bin/atkpython
export MPI=/home/edrl_05/QuantumATK/quantumatk/X-2025.06/mpi/bin/mpiexec.hydra
export MPIE=/home/edrl_05/QuantumATK/quantumatk/X-2025.06/mpi/bin/mpiexec
export MKL_DYNAMIC=TRUE
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
export LM_LICENSE_FILE="path"
export SNPSLMD_LICENSE_FILE="path"

${MPI} ${ATK} in.py > out.log 

8

General Questions and Answers / Re: Issues with AdaptiveDampingFactor in X-2025.06 version

« on: August 26, 2025, 14:27 »

If 0.01 also gives convergence issues.. try 0.01 or 0.02 with history steps reduced 12

9

General Questions and Answers / Re: NPT MD with Z-axis relaxation only (MD constraints)

« on: August 25, 2025, 09:55 »

What I understand is that you want to do NPT while fixing X and Y directions.
I think this is not possible.
Instead, what you can do is to use a NVT ensemble with vacuum in z direction. This will allow your system to relax in z direction but again this has some artifacts. One is that there will be surface effects at the termination in z direction. And one way to avoid that is using rigid atom constraint there.

10

General Questions and Answers / Re: NPT MD with Z-axis relaxation only (MD constraints)

« on: August 22, 2025, 08:10 »

Hi,
In MD block, you can then use NVT ensemble if you want to fix cell vectors. If you use NPT it will allow volume to change during MD.

11

General Questions and Answers / RAMAN Spectrum on monolayer MoS2

« on: August 22, 2025, 08:08 »

Dear Admin,
I am trying to calculate Raman Spectrum of monolayer MoS2. But I only see one peak around 396 cm^-1 whereas the experimental peaks are around 385 and 403 cm^-1. Kindly clarify the issue. I also tried changing polarization direction to 100. That gives three peaks but incorrect also. The script is as follows:

Code

# %% Molybdenite (1)

# Set up lattice
lattice = Hexagonal(3.1604*Angstrom, 40.0*Angstrom)

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

# Define coordinates
fractional_coordinates = [[ 0.333333333333,  0.666666666667,  0.5           ],
                          [ 0.666666666667,  0.333333333333,  0.460348625   ],
                          [ 0.666666666667,  0.333333333333,  0.539651375   ]]

# Set up configuration
molybdenite_1 = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

molybdenite_1_name = "Molybdenite (1)"


# %% Set LCAOCalculator

# %% LCAOCalculator

# ----------------------------------------
# Basis Set
# ----------------------------------------
basis_set = [
    BasisGGASG15.Sulfur_High,
    BasisGGASG15.Molybdenum_High,
]

k_point_sampling = MonkhorstPackGrid(na=13, nb=13)

numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=120.0 * Hartree, k_point_sampling=k_point_sampling
)

calculator = LCAOCalculator(
    basis_set=basis_set,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    checkpoint_handler=NoCheckpointHandler,
)


# %% Set Calculator

molybdenite_1.setCalculator(calculator)

molybdenite_1.update()

nlsave('Raman_SG15High.hdf5', molybdenite_1)


# %% OptimizeGeometry

restart_strategy = RestartFromTrajectory(
    trajectory_filename='Raman_SG15High.hdf5',
    object_id='optimize_trajectory',
)

optimized_configuration = OptimizeGeometry(
    configuration=molybdenite_1,
    max_forces=0.01 * eV / Angstrom,
    constraints=[FixStrain(True, True, True)],
    trajectory_filename='Raman_SG15High.hdf5',
    trajectory_object_id='optimize_trajectory',
    optimize_cell=False,
    restart_strategy=restart_strategy,
)

nlsave('Raman_SG15High.hdf5', optimized_configuration, object_id='optgeom')


# %% DynamicalMatrix

dynamical_matrix = DynamicalMatrix(
    configuration=optimized_configuration,
    filename='Raman_SG15High.hdf5',
    object_id='dm',
    calculator=calculator,
)
dynamical_matrix.update()


# %% SusceptibilityDerivatives

kpoints = MonkhorstPackGrid(na=23, nb=23, nc=2)

susceptibility_derivatives = SusceptibilityDerivatives(
    configuration=optimized_configuration,
    filename='Raman_SG15High.hdf5',
    object_id='sd',
    kpoints=kpoints,
)

susceptibility_derivatives.update()


# %% RamanSpectrum

raman_spectrum = RamanSpectrum(
    configuration=optimized_configuration,
    dynamical_matrix=dynamical_matrix,
    susceptibility_derivatives=susceptibility_derivatives,
    polarization_in=(0.0, 0.0, 1.0),
    polarization_out=(0.0, 0.0, 1.0),
    number_of_angles=None,
    polarization_orthogonal=None,
)
nlsave('Raman_SG15High.hdf5', raman_spectrum)

12

General Questions and Answers / Re: What is the efficient workflow (Calculator) for studying DDOS ,DOS? and visualiz

« on: August 21, 2025, 18:47 »

Try Device LCAO for DDOS and LCAO for DOS/PDOS

13

General Questions and Answers / Re: CALCULATED CARRIER CONCENTRATION

« on: August 21, 2025, 18:45 »

Hi,
You need to check if QATK support this function internally for carrier concentration. If not you can write a python script for calculating carrier concentration post DOS calculation.

14

General Questions and Answers / Re: energy convergence issue in perovskite LaMnO3

« on: August 21, 2025, 18:44 »

HI
Do u mean electron convergence or atomic force convergence?

For former, decrease the damping factor to 0.01 &/or history steps to 12.
For latter, try rattling of atoms around mean position.

15

General Questions and Answers / Re: Transport properties for Optimized Structures

« on: August 21, 2025, 18:40 »

Hi
This happens because QATK does not recognise the atoms in your electrode (left and right end) as repetitive after geometry optimization.
A way around is to use tag on few layers of atoms on left/right end and keep them fixed during optimization of central region but be careful this may introduce internal strain.
A better is way is to fix left side atoms of your material and keep right side atoms as rigid. Also, put a vacuum on the right side so that the rigid atoms can move into vacuum for proper relaxation. Then post relaxation remove vacuum using fit cell and you can easily create device.