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Topics - jalmeida

Pages: [1] 2
1
General Questions and Answers / Gold layers in central region
« on: February 4, 2025, 12:18 »
Hello  :D,

I work with molecular junctions using gold electrodes and I would like to know more about the increasing of gold layers in the central region for reability of optimized geometry and transmission function. What is the best approach:

1. Include gold layers in the electrode extension?
2. Include gold layers in the most inner part of central region (inside of "dashed lines")?

I believe if we do not optimize the junction the results will be the same. However, if we optimize, since the electrodes extension remains not relaxed, not gold layers enough in the most inner part could gives a geometry far from the reality. What is the case?

2
Hello,

Please, I would like to know if there are some analysis in the optimized junction to check its reliability. I know that we can perform a optimization using NEGF but it takes much longer. Do you know if there are some studies about the differences in the result from the two approaches, please?

For zero bias at least is enough to check if forces and total energy is going smoothly to the final geometry?

3
General Questions and Answers / IVCurve and IVCharacteristics
« on: February 3, 2025, 12:01 »
Hello,

I am using the IVCurve class for calculating an IV curve from -1 V to 1 V with step of 100 mV. I would like to understand how these calculations work. Here is what I believe is the step by step:

1. Do a self-consistent calculation for zero-bias
2. Do a self-consistent calculation at 100 mV reading the zero-bias
3. Do a self-consistent calculation at 200 mV reading the device configuration of 100 mV
4. And so on...
5. Do a transmission calculation for each self-consistent calculation already done.

However for negative bias I do not know if is the same procedure or for each negative bias, for example -100 mV, is reading the device configuration of the correspondent positive bias, i.e. 100 mV.

Is the procedure the same for IVCharacteristics class?

4
General Questions and Answers / perform_device_optimization
« on: January 28, 2025, 14:49 »
Dear all,

Please, how exactly is done the optimization when I set "perform_device_optimization=True" in OptimizeDeviceConfiguration class? Is a full optimization with NEGF instead of bulk as it is previously? Is that too much longer?


5
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

6
Dear  :D

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


7
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

8
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?




9
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  :)

10
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)

11
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.

12
Hello,

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






13
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


14
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


15
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

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