Topics

1

General Questions and Answers / Constrain angle metal/molecule in optimization geometry

« on: Yesterday at 11:05 »

Hello 

Please, I would like to optimize a system surface + molecule while maintaining the angle that the molecule makes with the surface. Is there a way to do it in QuantumATK?

I just found the class BondConstrain, but in that case I also have to constrain the bond length.

Best,
Joseane

2

General Questions and Answers / Interface dipole metal-molecule

« on: July 19, 2024, 18:09 »

Dear 

Please, How should I calculate the interface dipole? My system is a gold 111 surface + molecule.

I saw some tutorials which talk about interface dipole calculation from ElectronDifferenceDensity but without too much discussion (e.g. https://docs.quantumatk.com/tutorials/nisi2-si/nisi2-si.html).

Is this the best way to calculate it? Is there another way? How can I get the interface dipole value?

Best
Joseane

3

General Questions and Answers / Transmission pathway per kpoint

« on: July 18, 2024, 16:02 »

Dear 

Please, is there a way to calculate the transmission pathway for a specific kpoint? I saw the documentation, but the "kpoints" flag only accepts intergers, so maybe we can just set the number of points in A and B direction.

Joseane

4

General Questions and Answers / Spin-polarized calculation with Hybrid Functional

« on: February 19, 2024, 17:49 »

Hello,

I am trying to use the hybrid functional HSE06 to calculate the electronic structure of a spin-polarized molecular junction. The ATK version is 2021.06. However, I do not know how to give this in the input and I did not find in the documentation. Please, Could you help me?

5

General Questions and Answers / Molecular Dynamics for Devices and Boundary Conditions

« on: February 9, 2024, 15:09 »

Dear,

It is my first time trying to do Molecular Dynamics (MD) simulation and I have some questions that I did not find in details in the documentation and in the forum.

Please, Does ATK use always periodic boundary conditions in MD simulations, even for finite systems, e.g. molecules?

I tried to use MD for a device, so the electrodes and electrode repetitions are fixed automatically, right? Some atoms is going outside of the cell!

Is it better keep just the scattering region in a bulk configuration? Does cell size change in MD?

How can I choose a suitable unit cell? Should I increase the cell and keep the scattering region centralized or use a supercelll with the ATK tool "repeat cell" in all directions?

Thanks in advance 

6

General Questions and Answers / Adaptive grid

« on: February 6, 2024, 12:10 »

Dear,

I am simulating an electronic transmission function for a single molecular junction and part of the k-points used are not contributing well for the transmission values in some energies. So now I am trying to use the AdaptiveGrid that it takes much more time than the Monkhorst-Pack scheme. I decrease the maximum number of refinement steps (=7 now) to see if can be faster. How can I use the flag << function_values >> in this case if the transmission value for each k-point depends on the energy? The list of k-points for this function values is given in the flag << kpoints >>, right? How does it affect the kpoints chosen to construct the triangles? 

My initial code is below.

Code

device_configuration=nlread('/path/device.hdf5', DeviceConfiguration)[0]

# -------------------------------------------------------------
# Transmission Spectrum
# -------------------------------------------------------------

kpoints = AdaptiveGrid(
    kA_range=[-0.5, 0.5],
    kB_range=[-0.5, 0.5],
    tolerance=1e-3,
    error_measure=Absolute,
    number_of_initial_levels=3,
    maximum_number_of_levels=20,
    kpoints=None,
    intervals=None,
    triangles=None,
    function_values=None,
    )

transmission_spectrum = TransmissionSpectrum(
    configuration=device_configuration,
    energies=numpy.linspace(-1.0, 1.0, 800)*eV,
    kpoints=kpoints,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=RecursionSelfEnergy(),
    )
nlsave('device.hdf5', transmission_spectrum)
nlprint(transmission_spectrum)

7

General Questions and Answers / wide-band limit in molecular junctions

« on: December 19, 2023, 11:52 »

Hello 

Please, is it possible uses wide-band limit approximation to calculate electronic and phonon transport in ATK for molecular junctions? I found just an example with cnt but it uses semi-empirical model.

8

General Questions and Answers / Mulliken Charge for each optimization step

« on: December 14, 2023, 16:04 »

Hello,

Please, is it possible calculate automatically the Mulliken charge for each optimization step in QuantumATK?

9

General Questions and Answers / Phase/Magnitude of Transmission through Molecular Orbitals

« on: November 22, 2023, 16:34 »

Hello,

Please, How can I have access to the phase and transmission contribution of each molecular orbital in a molecular junction? I want to reproduce the pictures 6 and 7 of the paper <https://doi.org/10.1063/5.0141577>. I also attached the images from the paper.

Best,
Joseane

10

General Questions and Answers / Optimization in OneProbe Configuration

« on: November 21, 2023, 15:35 »

Hello 

I am trying to optimize a system surface+molecule using SurfaceConfiguration instead of slab method. However, I don't know the right way to proceed for the optimization. The calculator needs to be DeviceLCAOCalculator, but for optimization seems that I cannot use OptimizeDeviceConfiguration class. If I use the OptimizeGeometry I still need add constrains by myself to fix the atoms from left electrode and the electrode repetition?

For writing the input, comparing with two probe configuration script, the only difference is the boundary conditions, right?

Best,
Joseane

11

General Questions and Answers / optimize_cell flag Error

« on: October 4, 2023, 10:02 »

Hello,

I am trying to optimize a bulk configuration without change the unit cell. However I got an error that this flag does not belong to the class OptimizeGeometry! Please, What could be the problem?

My script:

bulk_configuration = nlread('/path/bulk.hdf5', BulkConfiguration)[0]

# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------

constraints = None

bulk_configuration = OptimizeGeometry(
    bulk_configuration,
    max_forces=0.02*eV/Ang,
    max_steps=50,
    max_step_length=0.2*Ang,
    constraints=constraints,
    optimize_cell=False,
    trajectory_filename='bulk_trajectory.hdf5',
    restart_strategy=RestartFromTrajectory(),
    disable_stress=True,
    optimizer_method=LBFGS(),
)
nlsave('bulk.hdf5', bulk_configuration)
nlprint(bulk_configuration)

The error:

File "bulk.py", line 9, in <module>
    bulk_configuration = OptimizeGeometry(
TypeError: OptimizeGeometry() got an unexpected keyword argument 'optimize_cell'
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 38
/tmp2/slurmd/job143810/slurm_script : ligne 50 : 261141 Erreur de segmentation  mpiexec -n 44 atkpython $job.py > $job.out

12

General Questions and Answers / DFTB basis set

« on: September 12, 2023, 16:23 »

Dear,

Please, is it possible set different basis set for different atoms in DFTB scheme? I have a system cluster-molecule-cluster, and I want to keep the symmetry closer to fcc bulk structure. I used the Wulff constructor and I want to optimise with clusters of different sizes. I suppose that for ~20 Au atoms the LCAOCalculator will be nice. However, more than 100 atoms for each cluster, I suppose it is better use DFTB. The gold is coordinate with sulphur and my molecule contains C, N , H and Fe. Seeing the AtomicData page on documentation, I believe that could be good use the basis set auorg-1-1 for the Au, mio-1-1 for H,C,N and S, and trans3d-0-1 for Fe. However, how can I do this?

13

General Questions and Answers / Basis set for Hydrogen

« on: August 29, 2023, 17:03 »

Dear all,

Please, what is the difference between use confined orbital for the Hydrogen atom and use directly the python class HydrogenOrbital? Are there some documentation explain better the HydrogenOrbital class (for example, the mathematical expression of the function )?

14

General Questions and Answers / HSE+U

« on: July 7, 2023, 17:13 »

Dear all,

Please, is it possible in QuantumATK use DFT+U with a Hybrid functional like HSE?

15

General Questions and Answers / QuantumATK doesn't read optimized structure

« on: March 30, 2023, 11:17 »

Dear all,

Please, I am trying to read the optimized structure of a junction but doesn't work. The part of the code is bellow:

device_configuration = nlread(filename='/home/jalmeida/MyProjects/junction/opt.hdf5',
                                                    class_type=DeviceConfiguration,
                                                    object_id='optimizedeviceconfiguration')

However, I got the error:

NL.ComputerScienceUtilities.Exceptions.NLTypeError: The parameter 'configuration' must be an instance of one of the following: MoleculeConfiguration, BulkConfiguration, SurfaceConfiguration, DeviceConfiguration.

The image of the objects is attached. probably I need to declare somehow the 'Optimized Configuration' to describe well where my DeviceConfiguration is. Thanks in advance!

Have a nice day,
SANTOS ALMEIDA, Joseane.