Messages

16

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.

17

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)

18

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

19

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.

20

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.

21

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.

22

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

« on: August 21, 2025, 18:36 »

HI
Unlesss u had checkpoint, I think u need to restart.

23

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

« on: August 21, 2025, 18:35 »

hi
Check under constraints in MD and optimization block and use tags for atoms you want to constraint.

24

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

« on: August 21, 2025, 18:32 »

Hi, Why would you choose it as adaptive instead of default 0.1 or below?
Incase you are facing convergence issues try it as 0.01

25

General Questions and Answers / DFT Phonon Transmission

« on: August 21, 2025, 18:30 »

Dear Admin,

I want to calculate phonon transmission across an interface of two 2D materials. The dimension are device are 7.83 A in periodic direction and a vacuum in out-of-plane direction and a total number of atoms as 153. In the dynamical matrix, it shows default repetitions as 3x1x1 however, which increases total atoms to 459.
This increases computational time very much beyond few weeks. Therefore, I used repetitions as 1x1x1.

I want to know is it the right approach and how would it affect my results if I don't use repetitions?
Also, would the approach be at-least useful for qualitative results?


Thanks

26

General Questions and Answers / Re: Problem in attaching the electrodes after device central optimization

« on: July 11, 2025, 13:46 »

Hi did you keep any layer fixed during optimistic?

27

General Questions and Answers / Re: GPU QATK

« on: June 28, 2025, 05:28 »

Thanks, Anders Blom,

It's resolved now. The error mentioned that it was not recognizing "qatk_gpu" when running a GPU simulation. Later, I found that the older version of Smart Keys didn't have any description of "qatk_gpu"
So, had to update the smart keys, and it worked nicely.

I might have some questions regarding the speedup. I am still testing it.

For someone facing the same issues, kindly redownload your SmartKeys from the Solvnet and replace them with the old ones.

28

General Questions and Answers / Re: GPU QATK

« on: June 25, 2025, 02:48 »

Update: I tried re-installing new SCL license but the issue still remains. It gives the same error.

29

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

« on: June 23, 2025, 19:14 »

Hi,
You don't need to use a vacuum when optimizing the bulk Ni or gold unit cell. Just optimize the bulk unit cells and then cleave 111 out of it.

Also, I see you have chosen a very less K-point sampling. The default for Ni is 12x12x1, and you have used 6x6x1.
Also, use a density mesh cutoff of around 110 Hartree.

The actual way to figure out these numbers is to calculate the total energy of the unit cell at various density mesh cutoff and K point sampling, and see at what values the total energy converges. Generally, the larger the supercell, the less K point sampling is required, and the smaller the cell, the larger the K point sampling.
Also, whether you want to optimize with/without cell optimization depends on which one gives you the right lattice parameters. This can you verify with literature or experiments.

30

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

« on: June 23, 2025, 07:29 »

Hi,

The tutorial you referred to uses a device configuration where you don't need to add a vacuum in the z direction; it takes care of it internally. However, the configuration you have shown in the pic is a bulk configuration. To optimize it as is given in the tutorial, you need to first convert your bulk configuration into a device, which you can do in the builder. In the builder, select your configuration from the stack, and then on the right, choose Device from the bulk.